Evidence Repository
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.233G>A (p.Arg78Gln)

CA1251448

876602 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 2315573e-5bfa-49d0-a748-32b214337932
Approved on: 2024-07-03
Published on: 2024-07-03

HGVS expressions

NM_000488.4:c.233G>A
NM_000488.4(SERPINC1):c.233G>A (p.Arg78Gln)
NC_000001.11:g.173914728C>T
CM000663.2:g.173914728C>T
NC_000001.10:g.173883866C>T
CM000663.1:g.173883866C>T
NC_000001.9:g.172150489C>T
NG_012462.1:g.7651G>A
ENST00000367698.4:c.233G>A
ENST00000367698.3:c.233G>A
ENST00000494024.1:n.459G>A
ENST00000617423.4:c.233G>A
NM_000488.3:c.233G>A
NM_001365052.1:c.89G>A
NM_001365052.2:c.89G>A
NM_001386302.1:c.233G>A
NM_001386303.1:c.314G>A
NM_001386304.1:c.233G>A
NM_001386305.1:c.233G>A
NM_001386306.1:c.233G>A

Uncertain Significance

Met criteria codes 1
BS1
Not Met criteria codes 3
PS4 PP3 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Thrombosis VCEP
The c.233G>A (NM_000488.3) variant in SERPINC1 is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 78 (p.Arg78Gln). The variant is reported at an allele frequency of 0.00003889 With the highest MAF of 0.0002540 (9/35440) in the South Asian population in gnomAD v2.1.1 meeting BS1 (>0.0002). In summary, based on the evidence available at this time, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Thrombosis Variant Curation Expert Panel for AT Deficiency for SERPINC1: BS1.
Met criteria codes
BS1
The variant is reported at an allele frequency of 0.00003889 With the highest MAF of 0.0002540 (9/35440) in the South Asian population in gnomAD v2.1.1 meeting BS1 (>0.0002). Update with gnomAD v4.1
Not Met criteria codes
PS4
1 proband with AT activity of 64-87 (had borderline median activity with normal antigen values) did not count
PP3
The variant has a REVEL score of 0.343, which does not meet criteria for PP3 (REVEL score >0.6)
BP4
The variant has a REVEL score of 0.343, which does not meet criteria for BP4 (REVEL score <0.3)
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