VCV001723735.8 - ClinVar

NM_006947.4(SRP72):c.25dup (p.Val9fs)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006947.4(SRP72):c.25dup (p.Val9fs)

Variation ID: 1723735 Accession: VCV001723735.8

Type and length

Duplication, 1 bp

Location

Cytogenetic: 4q12 4: 56467653-56467654 (GRCh38) [ NCBI UCSC ] 4: 57333819-57333820 (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	Nov 19, 2022	Oct 8, 2024	Dec 1, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_006947.4:c.25dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_008878.3:p.Val9fs	frameshift
NM_001267722.2:c.25dup	NP_001254651.1:p.Val9fs	frameshift
NM_006947.3:c.25dupG
NR_151856.2:n.44dup		non-coding transcript variant
NC_000004.12:g.56467660dup
NC_000004.11:g.57333826dup
NG_032796.1:g.5065dup
LRG_1151:g.5065dup
LRG_1151t1:c.25dup	LRG_1151p1:p.Val9fs

... more HGVS ... less HGVS

Protein change

V9fs

Other names

Canonical SPDI

NC_000004.12:56467653:GGGGGGG:GGGGGGGG

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

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.
LOC129992625	-	-	-	GRCh38	-	42
SRP72		-	-	GRCh38 GRCh37	565	620

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	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	Dec 1, 2023	RCV002306296.6
SRP72-related disorder	Uncertain significance (1)	no assertion criteria provided	Aug 5, 2024	RCV003408227.6

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.
Uncertain significance (Aug 10, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV002601354.3 First in ClinVar: Nov 19, 2022 Last updated: Aug 18, 2023	Comment: Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function … (more) Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not an established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge (less)
Uncertain significance (Dec 01, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004615084.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Comment: This sequence change creates a premature translational stop signal (p.Val9Glyfs9) in the SRP72 gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Val9Glyfs9) in the SRP72 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in SRP72 cause disease. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with SRP72-related conditions. ClinVar contains an entry for this variant (Variation ID: 1723735). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
Uncertain significance (Aug 05, 2024)	no assertion criteria provided Method: clinical testing	SRP72-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004115244.3 First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024	Comment: The SRP72 c.25dupG variant is predicted to result in a frameshift and premature protein termination (p.Val9Glyfs9). To our knowledge, this variant has not been reported … (more) The SRP72 c.25dupG variant is predicted to result in a frameshift and premature protein termination (p.Val9Glyfs9). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.012% of alleles in individuals of South Asian descent in gnomAD. Loss of function has not been conclusively established as a mechanism for SRP72-related disorders. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)

Comment:

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not an established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge

Comment:

This sequence change creates a premature translational stop signal (p.Val9Glyfs*9) in the SRP72 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in SRP72 cause disease. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with SRP72-related conditions. ClinVar contains an entry for this variant (Variation ID: 1723735). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

The SRP72 c.25dupG variant is predicted to result in a frameshift and premature protein termination (p.Val9Glyfs*9). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.012% of alleles in individuals of South Asian descent in gnomAD. Loss of function has not been conclusively established as a mechanism for SRP72-related disorders. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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.

Comment:

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 this variant ...

Record last updated Oct 13, 2024

ClinVar Genomic variation as it relates to human health

NM_006947.4(SRP72):c.25dup (p.Val9fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...