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]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC related information was provided by the message!
  • No CSPEC computer assertion could be determined for this classification!
  • See Evidence submitted by expert panel for details.

Variant: NM_000488.4(SERPINC1):c.-57G>A

CA10608400

293840 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 43c5651e-5486-479d-b365-1a71028f4407
Approved on: 2024-07-03
Published on: 2024-07-03

HGVS expressions

NM_000488.4:c.-57G>A
NM_000488.4(SERPINC1):c.-57G>A
NC_000001.11:g.173917316C>T
CM000663.2:g.173917316C>T
NC_000001.10:g.173886454C>T
CM000663.1:g.173886454C>T
NC_000001.9:g.172153077C>T
NG_012462.1:g.5063G>A
ENST00000367698.4:c.-57G>A
ENST00000367698.3:c.-57G>A
ENST00000494024.1:n.1G>A
ENST00000617423.4:c.-57G>A
NM_000488.3:c.-57G>A
NM_001365052.1:c.-370G>A
NM_001365052.2:c.-370G>A
NM_001386302.1:c.-57G>A
NM_001386303.1:c.-57G>A
NM_001386304.1:c.-57G>A
NM_001386305.1:c.-57G>A
NM_001386306.1:c.-57G>A
More

Likely Benign

Met criteria codes 3
BS1 BP7 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Thrombosis VCEP
The c.-57G>A (NM_000488.3) variant in SERPINC1 is in the 5' untranslated region (UTR) and changes nucleotide guanine to adenine. The minor allele frequency in gnomAD v2.1.1 is 0.0002868 (9/31380), which is higher than the ClinGen SERPINC1 threshold ([>0.0002]) for BS1, and therefore meets this criterion (BS1). SpliceAI predicts no impact on splicing, meeting criteria for BP4. SpliceAI predicts no impact on splicing and PhyloP gives a conservation score of -1.501 which is lower than the ClinGen SERPINC1 threshold (<0.1) for BP7, and therefore meets this criterion (BP7). 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: BS1, BP4, BP7.
Met criteria codes
BS1
The minor allele frequency in gnomAD v2.1.1 is 0.0002868 (9/31380) , which is higher than the ClinGen SERPINC1 threshold ([>0.0002]) for BS1, and therefore meets this criterion (BS1).
BP7
SpliceAI predicts no impact on splicing and PhyloP gives a conservation score of -1.501 which is lower than the ClinGen SERPINC1 threshold (<0.1) for BP7, and therefore meets this criterion (BP7).
BP4
SpliceAI predicts no impact on splicing, meeting criteria for BP4
Curation History
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