VCV000099889.12 - ClinVar

NM_201253.3(CRB1):c.2823G>A (p.Pro941=)

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.

(7)

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.

Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_201253.3(CRB1):c.2823G>A (p.Pro941=)

Variation ID: 99889 Accession: VCV000099889.12

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1q31.3 1: 197429595 (GRCh38) [ NCBI UCSC ] 1: 197398725 (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 20, 2014	Feb 28, 2024	Jan 14, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_201253.3:c.2823G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_957705.1:p.Pro941=	synonymous
NM_001193640.2:c.2487G>A	NP_001180569.1:p.Pro829=	synonymous
NM_001257965.2:c.2751G>A	NP_001244894.1:p.Pro917=	synonymous
NM_001257966.2:c.2129-6005G>A		intron variant
NR_047563.2:n.2776G>A		non-coding transcript variant
NR_047564.2:n.2984G>A		non-coding transcript variant
NC_000001.11:g.197429595G>A
NC_000001.10:g.197398725G>A
NG_008483.2:g.233134G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000001.11:197429594:G:A

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.

The Genome Aggregation Database (gnomAD) 0.00001

Trans-Omics for Precision Medicine (TOPMed) 0.00002

The Genome Aggregation Database (gnomAD), exomes 0.00004

Exome Aggregation Consortium (ExAC) 0.00005

Links

dbSNP: rs62645757 ClinGen: CA228018 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.
CRB1		-	-	GRCh38 GRCh37	1944	1969

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	not provided (1)	no classification provided	-	RCV000086329.3
Leber congenital amaurosis	Likely benign (1)	no assertion criteria provided	Mar 28, 2020	RCV001831901.1
Leber congenital amaurosis 8 Retinitis pigmentosa 12	Likely benign (1)	criteria provided, single submitter	Jan 14, 2024	RCV001080662.8
Leber congenital amaurosis 8 Pigmented paravenous retinochoroidal atrophy Retinitis pigmentosa 12	Likely benign (1)	criteria provided, single submitter	Jul 13, 2021	RCV002477255.1
Retinitis pigmentosa 12	Likely benign (1)	criteria provided, single submitter	Apr 11, 2023	RCV003453020.1
Pigmented paravenous retinochoroidal atrophy	Likely benign (1)	criteria provided, single submitter	Apr 11, 2023	RCV003453022.1
Leber congenital amaurosis 8	Likely benign (1)	criteria provided, single submitter	Apr 11, 2023	RCV003453021.1

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.
Likely benign (Jul 13, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Pigmented paravenous retinochoroidal atrophy Retinitis pigmentosa 12 Leber congenital amaurosis 8 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002802154.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Likely benign (Jan 14, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Leber congenital amaurosis 8 Retinitis pigmentosa 12 Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001090740.6 First in ClinVar: Dec 17, 2019 Last updated: Feb 28, 2024
Likely benign (Apr 11, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Leber congenital amaurosis 8 Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV004180083.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023
Likely benign (Apr 11, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Pigmented paravenous retinochoroidal atrophy Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV004180084.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023
Likely benign (Apr 11, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Retinitis pigmentosa 12 Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV004180085.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023
Likely benign (Mar 28, 2020)	no assertion criteria provided Method: clinical testing	Leber congenital amaurosis Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV002090187.1 First in ClinVar: Feb 13, 2022 Last updated: Feb 13, 2022
not provided (-)	no classification provided Method: not provided	not provided Affected status: not provided Allele origin: not provided	Retina International Accession: SCV000118475.1 First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014 Comment: http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_CRB1:c.2823G>A

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 rs62645757 ...

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 Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_201253.3(CRB1):c.2823G>A (p.Pro941=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs62645757 ...