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NM_015474.4(SAMHD1):c.1411-2A>G AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Nov 27, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003137627.4

Allele description [Variation Report for NM_015474.4(SAMHD1):c.1411-2A>G]

NM_015474.4(SAMHD1):c.1411-2A>G

Gene:
SAMHD1:SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q11.23
Genomic location:
Preferred name:
NM_015474.4(SAMHD1):c.1411-2A>G
Other names:
(Spliceacceptor); (Splice acceptor)
HGVS:
  • NC_000020.11:g.36904251T>C
  • NG_017059.1:g.52593A>G
  • NM_001363729.2:c.1411-2A>G
  • NM_001363733.2:c.1411-2A>G
  • NM_015474.4:c.1411-2A>GMANE SELECT
  • LRG_281t1:c.1411-2A>G
  • LRG_281:g.52593A>G
  • NC_000020.10:g.35532654T>C
  • NM_015474.3:c.1411-2A>G
Links:
dbSNP: rs515726141
NCBI 1000 Genomes Browser:
rs515726141
Molecular consequence:
  • NM_001363729.2:c.1411-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001363733.2:c.1411-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_015474.4:c.1411-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003827360Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 16, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005201557GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Nov 27, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Revvity Omics, Revvity, SCV003827360.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV005201557.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Published functional studies demonstrate skipping of exon 13 and degradation of the SAMHD1 protein in cell lysates from an affected individual (PMID: 21402907); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21633013, 31028937, 19525956, 28289923, 22461318, 34852373, 20301648, 21402907, 27943079)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024