VCV000782027.6 - ClinVar

NM_001037132.4(NRCAM):c.2699A>G (p.Glu900Gly)

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.

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_001037132.4(NRCAM):c.2699A>G (p.Glu900Gly)

Variation ID: 782027 Accession: VCV000782027.6

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 7q31.1 7: 108180375 (GRCh38) [ NCBI UCSC ] 7: 107820819 (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	Dec 17, 2019	Oct 8, 2024	Mar 9, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_001037132.4:c.2699A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001032209.1:p.Glu900Gly	missense
NM_001193582.2:c.2699A>G	NP_001180511.1:p.Glu900Gly	missense
NM_001193583.2:c.2642A>G	NP_001180512.1:p.Glu881Gly	missense
NM_001193584.2:c.2642A>G	NP_001180513.1:p.Glu881Gly	missense
NM_001371119.1:c.2642A>G	NP_001358048.1:p.Glu881Gly	missense
NM_001371122.1:c.2642A>G	NP_001358051.1:p.Glu881Gly	missense
NM_001371123.1:c.2699A>G	NP_001358052.1:p.Glu900Gly	missense
NM_001371124.1:c.2642A>G	NP_001358053.1:p.Glu881Gly	missense
NM_001371125.1:c.2354A>G	NP_001358054.1:p.Glu785Gly	missense
NM_001371126.1:c.2642A>G	NP_001358055.1:p.Glu881Gly	missense
NM_001371127.1:c.2696A>G	NP_001358056.1:p.Glu899Gly	missense
NM_001371128.1:c.2699A>G	NP_001358057.1:p.Glu900Gly	missense
NM_001371129.1:c.2642A>G	NP_001358058.1:p.Glu881Gly	missense
NM_001371130.1:c.2651A>G	NP_001358059.1:p.Glu884Gly	missense
NM_001371131.1:c.2699A>G	NP_001358060.1:p.Glu900Gly	missense
NM_001371132.1:c.2642A>G	NP_001358061.1:p.Glu881Gly	missense
NM_001371133.1:c.2651A>G	NP_001358062.1:p.Glu884Gly	missense
NM_001371134.1:c.2648A>G	NP_001358063.1:p.Glu883Gly	missense
NM_001371135.1:c.2642A>G	NP_001358064.1:p.Glu881Gly	missense
NM_001371136.1:c.2651A>G	NP_001358065.1:p.Glu884Gly	missense
NM_001371137.1:c.1742A>G	NP_001358066.1:p.Glu581Gly	missense
NM_001371138.1:c.2699A>G	NP_001358067.1:p.Glu900Gly	missense
NM_001371139.1:c.2642A>G	NP_001358068.1:p.Glu881Gly	missense
NM_001371140.1:c.2642A>G	NP_001358069.1:p.Glu881Gly	missense
NM_001371141.1:c.2642A>G	NP_001358070.1:p.Glu881Gly	missense
NM_001371142.1:c.2354A>G	NP_001358071.1:p.Glu785Gly	missense
NM_001371143.1:c.2354A>G	NP_001358072.1:p.Glu785Gly	missense
NM_001371144.1:c.2699A>G	NP_001358073.1:p.Glu900Gly	missense
NM_001371145.1:c.2642A>G	NP_001358074.1:p.Glu881Gly	missense
NM_001371146.1:c.2642A>G	NP_001358075.1:p.Glu881Gly	missense
NM_001371147.1:c.2354A>G	NP_001358076.1:p.Glu785Gly	missense
NM_001371148.1:c.2381A>G	NP_001358077.1:p.Glu794Gly	missense
NM_001371149.1:c.2699A>G	NP_001358078.1:p.Glu900Gly	missense
NM_001371150.1:c.2669A>G	NP_001358079.1:p.Glu890Gly	missense
NM_001371151.1:c.2651A>G	NP_001358080.1:p.Glu884Gly	missense
NM_001371152.1:c.2651A>G	NP_001358081.1:p.Glu884Gly	missense
NM_001371153.1:c.2699A>G	NP_001358082.1:p.Glu900Gly	missense
NM_001371154.1:c.2642A>G	NP_001358083.1:p.Glu881Gly	missense
NM_001371155.1:c.2642A>G	NP_001358084.1:p.Glu881Gly	missense
NM_001371156.1:c.2699A>G	NP_001358085.1:p.Glu900Gly	missense
NM_001371157.1:c.2651A>G	NP_001358086.1:p.Glu884Gly	missense
NM_001371158.1:c.2642A>G	NP_001358087.1:p.Glu881Gly	missense
NM_001371159.1:c.2669A>G	NP_001358088.1:p.Glu890Gly	missense
NM_001371160.1:c.2681A>G	NP_001358089.1:p.Glu894Gly	missense
NM_001371161.1:c.2699A>G	NP_001358090.1:p.Glu900Gly	missense
NM_001371162.1:c.2642A>G	NP_001358091.1:p.Glu881Gly	missense
NM_001371163.1:c.2642A>G	NP_001358092.1:p.Glu881Gly	missense
NM_001371164.1:c.2354A>G	NP_001358093.1:p.Glu785Gly	missense
NM_001371165.1:c.2642A>G	NP_001358094.1:p.Glu881Gly	missense
NM_001371166.1:c.2642A>G	NP_001358095.1:p.Glu881Gly	missense
NM_001371167.1:c.2642A>G	NP_001358096.1:p.Glu881Gly	missense
NM_001371168.1:c.2699A>G	NP_001358097.1:p.Glu900Gly	missense
NM_001371169.1:c.2699A>G	NP_001358098.1:p.Glu900Gly	missense
NM_001371170.1:c.2381A>G	NP_001358099.1:p.Glu794Gly	missense
NM_001371171.1:c.2651A>G	NP_001358100.1:p.Glu884Gly	missense
NM_001371172.1:c.2642A>G	NP_001358101.1:p.Glu881Gly	missense
NM_001371173.1:c.2699A>G	NP_001358102.1:p.Glu900Gly	missense
NM_001371174.1:c.2669A>G	NP_001358103.1:p.Glu890Gly	missense
NM_001371175.1:c.2651A>G	NP_001358104.1:p.Glu884Gly	missense
NM_001371176.1:c.2651A>G	NP_001358105.1:p.Glu884Gly	missense
NM_001371177.1:c.2642A>G	NP_001358106.1:p.Glu881Gly	missense
NM_001371178.1:c.2651A>G	NP_001358107.1:p.Glu884Gly	missense
NM_001371179.1:c.2381A>G	NP_001358108.1:p.Glu794Gly	missense
NM_001371180.1:c.2381A>G	NP_001358109.1:p.Glu794Gly	missense
NM_001371181.1:c.2642A>G	NP_001358110.1:p.Glu881Gly	missense
NM_001371182.1:c.2594A>G	NP_001358111.1:p.Glu865Gly	missense
NM_005010.5:c.2651A>G	NP_005001.3:p.Glu884Gly	missense
NR_163867.1:n.3167A>G		non-coding transcript variant
NR_163868.1:n.3167A>G		non-coding transcript variant
NR_163869.1:n.3167A>G		non-coding transcript variant
NR_163870.1:n.3248A>G		non-coding transcript variant
NR_163871.1:n.3246A>G		non-coding transcript variant
NC_000007.14:g.108180375T>C
NC_000007.13:g.107820819T>C
NG_029898.2:g.281343A>G

... more HGVS ... less HGVS

Protein change

E794G, E881G, E884G, E890G, E894G, E899G, E581G, E785G, E883G, E865G, E900G

Other names

Canonical SPDI

NC_000007.14:108180374:T:C

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.

0.00240 (C)

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

1000 Genomes Project 30x 0.00219

1000 Genomes Project 0.00240

Trans-Omics for Precision Medicine (TOPMed) 0.00376

Exome Aggregation Consortium (ExAC) 0.00383

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00392

The Genome Aggregation Database (gnomAD), exomes 0.00417

The Genome Aggregation Database (gnomAD) 0.00436

Links

dbSNP: rs34721383 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.
NRCAM		-	-	GRCh38 GRCh37	122	147

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	Mar 9, 2018	RCV000963354.4
NRCAM-related disorder	Likely benign (1)	no assertion criteria provided	Jun 12, 2019	RCV004535928.2

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 (Mar 09, 2018)	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: SCV001110505.1 First in ClinVar: Dec 17, 2019 Last updated: Dec 17, 2019
Likely benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005221473.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Likely benign (Jun 12, 2019)	no assertion criteria provided Method: clinical testing	NRCAM-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004730901.2 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 rs34721383 ...

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 25, 2024

ClinVar Genomic variation as it relates to human health

NM_001037132.4(NRCAM):c.2699A>G (p.Glu900Gly)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs34721383 ...