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.408+4C>T

CA1251431

876601 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
UUID: 561e873f-4335-45d7-bae2-24cb46334c95
Approved on: 2023-07-25
Published on: 2023-09-29

HGVS expressions

NM_000488.4:c.408+4C>T
NM_000488.4(SERPINC1):c.408+4C>T
NC_000001.11:g.173914549G>A
CM000663.2:g.173914549G>A
NC_000001.10:g.173883687G>A
CM000663.1:g.173883687G>A
NC_000001.9:g.172150310G>A
NG_012462.1:g.7830C>T
ENST00000367698.4:c.408+4C>T
ENST00000367698.3:c.408+4C>T
ENST00000487183.1:n.113+4C>T
ENST00000494024.1:n.634+4C>T
ENST00000617423.4:c.408+4C>T
NM_000488.3:c.408+4C>T
NM_001365052.1:c.264+4C>T
NM_001365052.2:c.264+4C>T
NM_001386302.1:c.408+4C>T
NM_001386303.1:c.489+4C>T
NM_001386304.1:c.408+4C>T
NM_001386305.1:c.408+4C>T
NM_001386306.1:c.408+4C>T
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Likely Benign

Met criteria codes 2
BS1 BP4
Not Met criteria codes 1
BP7

Evidence Links 0

Expert Panel

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.408+4C>T variant is an intronic variant reported at a POPMAX FAF of 0.0003794 in the South Asian population (18/30616 alleles) meeting BS1 criteria. SpliceAI and VarSEAK predict no splicing impact for this variant; however the nucleotide may be conserved based on PhyloP and PhastCons scores (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 AT Deficiency for SERPINC1: BS1, BP4.
Met criteria codes
BS1
The c.408+4C>T intronic variant is reported at a POPMAX FAF of 0.0003794 in the South Asian population (18/30616 alleles) and meets criteria for BS1.
BP4
SpliceAI and VarSEAK predict no splicing impact.
Not Met criteria codes
BP7
While no splicing impact is predicted by SpliceAI and MaxEntScan, the nucleotide may be moderately conserved, with PhyloP score of 0.53 and PhastCons score of 0.0077. BP7 criteria not met.
Curation History
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