VCV000376895.9 - ClinVar

NM_001321218.2(B9D1):c.473-1G>C

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.

(5)

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.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Benign(1); Likely benign(2)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001321218.2(B9D1):c.473-1G>C

Variation ID: 376895 Accession: VCV000376895.9

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17p11.2 17: 19337749 (GRCh38) [ NCBI UCSC ] 17: 19241062 (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	Mar 8, 2017	Oct 8, 2024	Dec 18, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001321218.2:c.473-1G>C		splice acceptor
NM_001321219.2:c.405-1G>C		splice acceptor
NM_001368769.2:c.113-1G>C		splice acceptor
NC_000017.11:g.19337749C>G
NC_000017.10:g.19241062C>G
NG_031885.2:g.45445G>C
LRG_686:g.45445G>C

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000017.11:19337748:C:G

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.

0.01338 (G)

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

Trans-Omics for Precision Medicine (TOPMed) 0.01229

1000 Genomes Project 30x 0.01327

1000 Genomes Project 0.01338

Exome Aggregation Consortium (ExAC) 0.00236

The Genome Aggregation Database (gnomAD), exomes 0.00284

The Genome Aggregation Database (gnomAD) 0.01140

Links

ClinGen: CA8440035 dbSNP: rs73980009 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.
B9D1		-	-	GRCh38 GRCh37	201	338

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.
not provided	Likely benign (2)	criteria provided, multiple submitters, no conflicts	Dec 23, 2018	RCV000428981.12
Joubert syndrome 27	Likely pathogenic (1)	criteria provided, single submitter	Sep 26, 2019	RCV001291732.10
not specified	Benign (1)	criteria provided, single submitter	Dec 18, 2023	RCV004017610.1
B9D1-related disorder	Likely benign (1)	no assertion criteria provided	Jun 5, 2019	RCV004555575.2

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.
Likely Benign (Jan 31, 2017)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: not provided Allele origin: germline	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics Accession: SCV000510825.1 First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017	Comment: Converted during submission to Likely benign.
Likely pathogenic (Sep 26, 2019)	criteria provided, single submitter (NYGC Assertion Criteria 2020) Method: clinical testing	Joubert syndrome 27 (Autosomal recessive inheritance) Affected status: unknown Allele origin: germline	New York Genome Center Study: CSER-NYCKidSeq Accession: SCV001480320.1 First in ClinVar: Feb 20, 2021 Last updated: Feb 20, 2021	Clinical Features: Intellectual disability (present) , Seizure (present) , Autism (present) , Cerebral visual impairment (present) Secondary finding: no
Likely benign (Dec 23, 2018)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001813191.1 First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021
Benign (Dec 18, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine Accession: SCV004847391.1 First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024	Comment: The c.473-1G>C variant in B9D1 is classified as benign because it has been identified in 3.5% (1469/41430) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). ACMG/AMP … (more) The c.473-1G>C variant in B9D1 is classified as benign because it has been identified in 3.5% (1469/41430) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). ACMG/AMP Criteria applied: BA1. (less)
Likely benign (Jun 05, 2019)	no assertion criteria provided Method: clinical testing	B9D1-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004751494.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs73980009 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NM_001321218.2(B9D1):c.473-1G>C

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs73980009 ...