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]

Link to SEPIO compliant JSON-LD document

Variant: NM_000488.4(SERPINC1):c.1350C>T (p.Asn450=)

CA1251215

2415371 (ClinVar)

Gene: SERPINC1

Condition: antithrombin III deficiency

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 903d21fc-3949-409e-bf5d-5ce6bb201e88

HGVS expressions

NM_000488.4:c.1350C>T

NM_000488.4(SERPINC1):c.1350C>T (p.Asn450=)

NC_000001.11:g.173903934G>A

CM000663.2:g.173903934G>A

NC_000001.10:g.173873072G>A

CM000663.1:g.173873072G>A

NC_000001.9:g.172139695G>A

NG_012462.1:g.18445C>T

ENST00000367698.4:c.1350C>T

ENST00000367698.3:c.1350C>T

ENST00000617423.4:c.735C>T

NM_000488.3:c.1350C>T

NM_001365052.1:c.1206C>T

NM_001365052.2:c.1206C>T

NM_001386302.1:c.1473C>T

NM_001386303.1:c.1431C>T

NM_001386304.1:c.1329C>T

NM_001386305.1:c.1293C>T

NM_001386306.1:c.1134C>T

Likely Benign

BS1 BP4

BP7

Evidence Links 0

Expert Panel

Thrombosis VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Thrombosis VCEP

The c.1350C>T (NM_000488.4) variant in SERPINC1 does not code for a different amino acid (p.Asn450=). The variant is reported at a POPMAX FAF of 0.0002003 (5/24962) in the African/African American population in gnomAD v2.1.1 meeting BS1 criteria (allele frequency > 0.0002 w/min of 5 alleles). SpliceAI predicts no splicing impact for this variant meeting BP4. 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.

BS1

The variant is reported at a POPMAX FAF of 0.0002003 (5/24962) in the African/African American population in gnomAD v2.1.1 meeting BS1 criteria (allele frequency > 0.0002 w/min of 5 alleles).

BP4

SpliceAI predicts no splicing impact for this variant.

BP7

The variant is not predicted to cause a splicing impact, but the nucleotide is weakly/moderately conserved with a PhyloP score of 0.649 and a PhastCons score of ~1. BP7 is not met.

Approved on: 2024-01-25

Published on: 2024-01-25

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