Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_000488.4(SERPINC1):c.1218+27G>C

CA1251245

1261351 (ClinVar)

Gene: SERPINC1

Condition: antithrombin III deficiency

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: b3e9ed5b-7c1b-4da4-92ee-8d314906046a

Approved on: 2023-07-25

Published on: 2023-09-29

HGVS expressions

NM_000488.4:c.1218+27G>C

NM_000488.4(SERPINC1):c.1218+27G>C

NC_000001.11:g.173907423C>G

CM000663.2:g.173907423C>G

NC_000001.10:g.173876561C>G

CM000663.1:g.173876561C>G

NC_000001.9:g.172143184C>G

NG_012462.1:g.14956G>C

ENST00000367698.4:c.1218+27G>C

ENST00000367698.3:c.1218+27G>C

ENST00000617423.4:c.603+27G>C

NM_000488.3:c.1218+27G>C

NM_001365052.1:c.1074+27G>C

NM_001365052.2:c.1074+27G>C

NM_001386302.1:c.1341+27G>C

NM_001386303.1:c.1299+27G>C

NM_001386304.1:c.1197+27G>C

NM_001386305.1:c.1161+27G>C

NM_001386306.1:c.1002+27G>C

Benign

BP7 BP4 BA1

PS4

Evidence Links 0

Expert Panel

Thrombosis VCEP

Criteria Specification Information

Criteria Specification: ClinGen Thrombosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SERPINC1 Version 1.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Thrombosis VCEP

The NM_000488.4:c.1218+27G>C variant is reported at an Popmax FAF MAF of 0.2409 (4979/19948 alleles) in the East Asian population in the genomes in gnomAD v2.1.1 with a total of 2550 homozygotes, meeting BA1 criteria of FAF >= 0.002. The variant is not predicted to cause a splicing impact by by SpliceAI and VARSEAK, and the nucleotide is not conserved with a PhyloP score of -1.65 and a PhastCons score of ~0. 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, BP4, BP7.

BP7

The variant is not predicted to cause a splicing impact, and the nucleotide is not conserved with a PhyloP score of -1.65 and a PhastCons score of ~0. BP7 is met.

BP4

No splicing impact is predicted by SpliceAI and VARSEAK

BA1

The c.981A>G (p.Val327=) variant is reported at an Popmax FAF MAF of 0.2409 (4979/19948 alleles) in the East Asian population in the genomes in gnomAD v2.1.1 with a total of 2550 homozygotes, meeting BA1 criteria of FAF >= 0.002

PS4

The variant is reported as a polymorphism in reports evaluating risk alleles in genes predisposing to disease.

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