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.594T>C (p.Tyr198=)

CA1251397

529743 (ClinVar)

Gene: SERPINC1

Condition: antithrombin III deficiency

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 8fd403ed-2566-4ae7-b84c-c53ab771fdec

Approved on: 2024-08-16

Published on: 2024-08-21

HGVS expressions

NM_000488.4:c.594T>C

NM_000488.4(SERPINC1):c.594T>C (p.Tyr198=)

NC_000001.11:g.173911829A>G

CM000663.2:g.173911829A>G

NC_000001.10:g.173880967A>G

CM000663.1:g.173880967A>G

NC_000001.9:g.172147590A>G

NG_012462.1:g.10550T>C

ENST00000367698.4:c.594T>C

ENST00000367698.3:c.594T>C

ENST00000487183.1:n.299T>C

ENST00000617423.4:c.559+35T>C

NM_000488.3:c.594T>C

NM_001365052.1:c.450T>C

NM_001365052.2:c.450T>C

NM_001386302.1:c.594T>C

NM_001386303.1:c.675T>C

NM_001386304.1:c.594T>C

NM_001386305.1:c.594T>C

NM_001386306.1:c.409-938T>C

Likely Benign

BP7 BP4

BS1 PM2

Evidence Links 0

Expert Panel

Thrombosis VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Thrombosis VCEP

The c.594T>C (NM_000488.4) variant in SERPINC1 does not code for a different amino acid (p.Tyr198=). SpliceAI predicts no splicing impact for this variant meeting BP4. The variant is not predicted to cause a splicing impact and the nucleotide is weakly/moderately conserved with a PhyloP score of 0.025 meeting BP7 criteria (PhyloP < 0.1). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Thrombosis Variant Curation Expert Panel for SERPINC1: BP4, BP7.

BP7

The variant is not predicted to cause a splicing impact and the nucleotide is weakly/moderately conserved with a PhyloP score of 0.025 meeting BP7 criteria (PhyloP < 0.1).

BP4

SpliceAI predicts no splicing impact for this variant meeting BP4.

BS1

The highest population minor allele frequency in gnomAD v2.1.1 is 0.00007912 (9/113758 alleles) in the European population, which is lower than the ClinGen SERPINC1 threshold ([>0.0002]) for BS1.

PM2

The highest population minor allele frequency in gnomAD v2.1.1 is 0.00007912 (9/113758 alleles) in the European population, which is higher than the ClinGen SERPINC1 threshold ([<0.00002]) for PM2.

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