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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  • See Evidence submitted by expert panel for details.

Variant: NM_000488.4(SERPINC1):c.1254C>T (p.Thr418=)

CA1251226

1144693 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 091c5937-d5f5-4170-8a72-01f14c2794bc
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_000488.4:c.1254C>T
NM_000488.4(SERPINC1):c.1254C>T (p.Thr418=)
NC_000001.11:g.173904030G>A
CM000663.2:g.173904030G>A
NC_000001.10:g.173873168G>A
CM000663.1:g.173873168G>A
NC_000001.9:g.172139791G>A
NG_012462.1:g.18349C>T
ENST00000367698.4:c.1254C>T
ENST00000367698.3:c.1254C>T
ENST00000617423.4:c.639C>T
NM_000488.3:c.1254C>T
NM_001365052.1:c.1110C>T
NM_001365052.2:c.1110C>T
NM_001386302.1:c.1377C>T
NM_001386303.1:c.1335C>T
NM_001386304.1:c.1233C>T
NM_001386305.1:c.1197C>T
NM_001386306.1:c.1038C>T

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 2
PM2 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Thrombosis VCEP
The c.1254C>T (NM_000488.4) variant in SERPINC1 does not code for a different amino acid (p.Thr418=). 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 -1.569 and a PhastCons score of 0.013 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.
Met criteria codes
BP7
The variant is not predicted to cause a splicing impact and the nucleotide is weakly/moderately conserved with a PhyloP score of -1.569 and a PhastCons score of 0.013 meeting BP7 criteria (PhyloP < 0.1).
BP4
SpliceAI predicts no splicing impact for this variant meeting BP4.
Not Met criteria codes
PM2
The variant is reported at a POPMAX FAF of 0.0001960 (6/30616) in the South Asian population in gnomAD v2.1.1 which does not meet PM2_supporting criteria (MAF < 2.0 X 10-5 in gnomAD).
BS1
The variant is reported at a POPMAX FAF of 0.0001960 (6/30616) in the South Asian population in gnomAD v2.1.1 which does not meet BS1 criteria (allele frequency > 0.0002 w/min of 5 alleles).
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