VCV000156975.1 - ClinVar

NM_004536.3(NAIP):c.569-263_668+1406del

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

not provided

no classification provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_004536.3(NAIP):c.569-263_668+1406del

Variation ID: 156975 Accession: VCV000156975.1

Type and length

Deletion, 1,769 bp

Location

Cytogenetic: 5q13.2 5: 71009869-71011637 (GRCh38) [ NCBI UCSC ] 5: 70305696-70307464 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 26, 2015	Feb 26, 2015

HGVS

Nucleotide	Protein	Molecular consequence
NM_004536.3:c.569-263_668+1406del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor splice donor
NM_001346870.2:c.569-263_668+1406del		splice acceptor splice donor
NM_022892.2:c.183-7780_183-6012del		intron variant
NC_000005.10:g.71009869_71011637del
NC_000005.9:g.70305696_70307464del
NG_008724.1:g.18478_20246del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA212117 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NAIP		-	-	GRCh38 GRCh38 GRCh38 GRCh38 GRCh37	12	69

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Normal pregnancy	not provided (1)	no classification provided	-	RCV000161401.3
Large for gestational age	not provided (1)	no classification provided	-	RCV000161402.3
Gestational diabetes mellitus uncontrolled	not provided (1)	no classification provided	-	RCV000161403.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
not provided (-)	no classification provided Method: case-control	Normal pregnancy Affected status: yes Allele origin: unknown	Institute of Molecular and Cell Biology, University of Tartu Study: Kasak2014 Accession: SCV000191358.1 First in ClinVar: Feb 26, 2015 Last updated: Feb 26, 2015 Comment: The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal … (more) The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal blood DNA drawn from healthy pregnant women during 1st or 2nd trimester and (ii) maternal and paternal blood DNA drawn at term pregnancy cases representing normal and complicated gestations (severe preeclampsia, PE; gestational diabetes, GD; small-for-gestational age newborn, SGA; large-for-gestational age newborn, LGA). We performed CNV calling based on genome-wide genotyping dataset (Illumina HumanOmniExpress-24-v1 BeadChip) by applying three algorithms, QuantiSNP, GADA (Genome Alteration Detection Algorithm) and CNstream in parallel. The acquired CNV calls were merged with HD-CNV (Hotspot Detector for Copy Number Variants) program and only the CNVs predicted by at least two programs, were considered in subsequent analysis. (less)	Publications: PubMed (1) PubMed: 25666259 Observation 1: Sex: mixed Tissue: Blood Method: Genomic DNA copy number estimation from GenomeStudio-normalised genotyping microarray data (probe signal intensity). Using Illumina's baseline data for microarray signal intensity normalisation, QuantiSNP default baseline data (OB-HMM parameter values) for CNV calling. Observation 2: Sex: female Tissue: Blood Method: Genomic DNA copy number estimation from GenomeStudio-normalised genotyping microarray data (probe signal intensity). Using Illumina's baseline data for microarray signal intensity normalisation, QuantiSNP default baseline data (OB-HMM parameter values) for CNV calling.
not provided (-)	no classification provided Method: case-control	Large for gestational age Affected status: yes Allele origin: unknown	Institute of Molecular and Cell Biology, University of Tartu Study: Kasak2014 Accession: SCV000191359.1 First in ClinVar: Feb 26, 2015 Last updated: Feb 26, 2015 Comment: The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal … (more) The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal blood DNA drawn from healthy pregnant women during 1st or 2nd trimester and (ii) maternal and paternal blood DNA drawn at term pregnancy cases representing normal and complicated gestations (severe preeclampsia, PE; gestational diabetes, GD; small-for-gestational age newborn, SGA; large-for-gestational age newborn, LGA). We performed CNV calling based on genome-wide genotyping dataset (Illumina HumanOmniExpress-24-v1 BeadChip) by applying three algorithms, QuantiSNP, GADA (Genome Alteration Detection Algorithm) and CNstream in parallel. The acquired CNV calls were merged with HD-CNV (Hotspot Detector for Copy Number Variants) program and only the CNVs predicted by at least two programs, were considered in subsequent analysis. (less)	Publications: PubMed (1) PubMed: 25666259 Sex: mixed Tissue: Blood Method: Genomic DNA copy number estimation from GenomeStudio-normalised genotyping microarray data (probe signal intensity). Using Illumina's baseline data for microarray signal intensity normalisation, QuantiSNP default baseline data (OB-HMM parameter values) for CNV calling.
not provided (-)	no classification provided Method: case-control	Gestational diabetes mellitus uncontrolled Affected status: yes Allele origin: unknown	Institute of Molecular and Cell Biology, University of Tartu Study: Kasak2014 Accession: SCV000191360.1 First in ClinVar: Feb 26, 2015 Last updated: Feb 26, 2015 Comment: The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal … (more) The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal blood DNA drawn from healthy pregnant women during 1st or 2nd trimester and (ii) maternal and paternal blood DNA drawn at term pregnancy cases representing normal and complicated gestations (severe preeclampsia, PE; gestational diabetes, GD; small-for-gestational age newborn, SGA; large-for-gestational age newborn, LGA). We performed CNV calling based on genome-wide genotyping dataset (Illumina HumanOmniExpress-24-v1 BeadChip) by applying three algorithms, QuantiSNP, GADA (Genome Alteration Detection Algorithm) and CNstream in parallel. The acquired CNV calls were merged with HD-CNV (Hotspot Detector for Copy Number Variants) program and only the CNVs predicted by at least two programs, were considered in subsequent analysis. (less)	Publications: PubMed (1) PubMed: 25666259 Observation 1: Sex: mixed Tissue: Blood Method: Genomic DNA copy number estimation from GenomeStudio-normalised genotyping microarray data (probe signal intensity). Using Illumina's baseline data for microarray signal intensity normalisation, QuantiSNP default baseline data (OB-HMM parameter values) for CNV calling. Observation 2: Sex: mixed Tissue: Blood Method: Genomic DNA copy number estimation from GenomeStudio-normalised genotyping microarray data (probe signal intensity). Using Illumina's baseline data for microarray signal intensity normalisation, QuantiSNP default baseline data (OB-HMM parameter values) for CNV calling.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Extensive load of somatic CNVs in the human placenta.	Kasak L	Scientific reports	2015	PMID: 25666259

Text-mined citations for this variant ...

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_004536.3(NAIP):c.569-263_668+1406del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...