VCV000018173.1 - ClinVar

NM_000014.6(A2M):c.2125+1_2126-1del

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.

(1)

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.

Benign

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000014.6(A2M):c.2125+1_2126-1del

Variation ID: 18173 Accession: VCV000018173.1

Type and length

Deletion, 1,393 bp

Location

Cytogenetic: 12p13.31 12: 9093580-9094972 (GRCh38) [ NCBI UCSC ] 12: 9246176-9247568 (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	Apr 4, 2013	Apr 4, 2013	Jan 1, 1992

HGVS

Nucleotide	Protein	Molecular consequence
NM_000014.6:c.2125+1_2126-1del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor splice donor
NM_001347423.2:c.2125+1_2126-1del		splice acceptor splice donor
NM_001347424.2:c.1825+1_1826-1del		splice acceptor splice donor
NM_001347425.2:c.1675+1_1676-1del		splice acceptor splice donor
NC_000012.12:g.9093581_9094973del
NC_000012.11:g.9246177_9247569del
NG_011717.2:g.25991_27383del
LRG_591:g.25991_27383del
LRG_591t1:c.2125+1_2126-1del

... more HGVS ... less HGVS

Protein change

Other names

A2M, IVS1DEL
IVS1DEL

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: CA127862 OMIM: 103950.0003 VarSome

Comment on variant

Deletion of intron 17 from A2M (NG_011717.1)

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.
A2M		-	-	GRCh38 GRCh37	-	146
KLRG1		-	-	GRCh38 GRCh37	9	242

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.
ALPHA-2-MACROGLOBULIN POLYMORPHISM	Benign (1)	no assertion criteria provided	Jan 1, 1992	RCV000019804.2

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.
Benign (Jan 01, 1992)	no assertion criteria provided Method: literature only	ALPHA-2-MACROGLOBULIN POLYMORPHISM Affected status: not provided Allele origin: germline	OMIM Accession: SCV000040102.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 1370808 Comment on evidence: In 1 healthy individual, Poller et al. (1992) found a deletion of the intron that ordinarily separates exons 1 and 2. As a result, the … (more) In 1 healthy individual, Poller et al. (1992) found a deletion of the intron that ordinarily separates exons 1 and 2. As a result, the 2 exons that code the bait domain of the alpha-2-macroglobulin gene were fused. (less)

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
Cloning of the human alpha 2-macroglobulin gene and detection of mutations in two functional domains: the bait region and the thiolester site.	Poller W	Human genetics	1992	PMID: 1370808

Text-mined citations for this variant ...

Record last updated Feb 07, 2023

ClinVar Genomic variation as it relates to human health

NM_000014.6(A2M):c.2125+1_2126-1del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...