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

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

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.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.
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 0.025 meeting BP7 criteria (PhyloP < 0.1).
BP4
SpliceAI predicts no splicing impact for this variant meeting BP4.
Not Met criteria codes
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.
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.
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