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]

Variant: NM_000488.4(SERPINC1):c.1154-5T>C

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA335750

215473 (ClinVar)

Gene: SERPINC1

Condition: antithrombin III deficiency

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 85806050-7cf6-4d52-a2a8-a7a0df5787dd

Approved on: 2023-07-25

Published on: 2023-09-29

HGVS expressions

NM_000488.4:c.1154-5T>C

NM_000488.4(SERPINC1):c.1154-5T>C

NC_000001.11:g.173907519A>G

CM000663.2:g.173907519A>G

NC_000001.10:g.173876657A>G

CM000663.1:g.173876657A>G

NC_000001.9:g.172143280A>G

NG_012462.1:g.14860T>C

ENST00000367698.4:c.1154-5T>C

ENST00000367698.3:c.1154-5T>C

ENST00000617423.4:c.560-26T>C

NM_000488.3:c.1154-5T>C

NM_001365052.1:c.1010-5T>C

NM_001365052.2:c.1010-5T>C

NM_001386302.1:c.1277-5T>C

NM_001386303.1:c.1235-5T>C

NM_001386304.1:c.1133-5T>C

NM_001386305.1:c.1097-5T>C

NM_001386306.1:c.938-5T>C

Likely Benign

BP4 BS1

Evidence Links 0

Expert Panel

Thrombosis VCEP

Criteria Specification Information

Criteria Specification: ClinGen Thrombosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SERPINC1 Version 1.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Thrombosis VCEP

The NM_000488.4(SERPINC1):c.1154-5T>C variant is an intronic change that has a frequency of 0.03% in South Asians with 11 alleles (gnomAD v2.1.1). No splicing disruption prediction is noted per SpliceAI and varSEAK, but the nucleotide may be moderately conserved. 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.

BP4

No splicing disruption prediction per SpliceAI and varSEAK. REVEL score is not applicable for this variant type. Moderate conservation, higher than PhyloP cutoff.

BS1

This variant has a frequency of 0.03% on South Asians with 11 alleles (gnomAD v2.1.1). Overall MAF is 0.008% (00.00008131).

Curation History

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