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NM_000488.4(SERPINC1):c.42-18C>T AND Hereditary antithrombin deficiency

Germline classification:
Benign (2 submissions)
Last evaluated:
Jul 25, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV002106445.6

Allele description [Variation Report for NM_000488.4(SERPINC1):c.42-18C>T]

NM_000488.4(SERPINC1):c.42-18C>T

Gene:
SERPINC1:serpin family C member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q25.1
Genomic location:
Preferred name:
NM_000488.4(SERPINC1):c.42-18C>T
HGVS:
  • NC_000001.11:g.173914937G>A
  • NG_012462.1:g.7442C>T
  • NM_000488.4:c.42-18C>TMANE SELECT
  • NM_001365052.2:c.-103-18C>T
  • NM_001386302.1:c.42-18C>T
  • NM_001386303.1:c.123-18C>T
  • NM_001386304.1:c.42-18C>T
  • NM_001386305.1:c.42-18C>T
  • NM_001386306.1:c.42-18C>T
  • LRG_577:g.7442C>T
  • NC_000001.10:g.173884075G>A
Links:
dbSNP: rs2227599
NCBI 1000 Genomes Browser:
rs2227599
Molecular consequence:
  • NM_000488.4:c.42-18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001365052.2:c.-103-18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386302.1:c.42-18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386303.1:c.123-18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386304.1:c.42-18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386305.1:c.42-18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386306.1:c.42-18C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Hereditary antithrombin deficiency
Synonyms:
Antithrombin III deficiency; Thrombophilia due to antithrombin III deficiency; Reduced antithrombin III activity; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013144; MedGen: C0272375; OMIM: 613118; Human Phenotype Ontology: HP:0001976

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002440745Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Benign
(Feb 1, 2024) 		germlineclinical testing

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

SCV004037402Clingen Thrombosis Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen ACMG Specifications SERPINC1 V1.0.0)		Benign
(Jul 25, 2023) 		germlinecuration

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002440745.3

#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 Clingen Thrombosis Variant Curation Expert Panel, ClinGen, SCV004037402.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_000488.4:c.42-18C>T variant is reported at a popmax FAF of 0.0771 and the highest MAF of 0.08248 (8%; 1996/24200 alleles with 85 homozygotes) in the African/African American population in gnomAD v2.1.1, meeting criteria for BA1 (MAF >0.002). The variant is reported in 2 individuals with normal antithrombin levels. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Thrombosis Variant Curation Expert Panel for SERPINC1: BA1, BS2.

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

Last Updated: Feb 20, 2024