rs677
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4BA1BP7
This summary comes from the ClinGen Evidence Repository: The NM_000488.4:c.1218+27G>C variant is reported at an Popmax FAF MAF of 0.2409 (4979/19948 alleles) in the East Asian population in the genomes in gnomAD v2.1.1 with a total of 2550 homozygotes, meeting BA1 criteria of FAF >= 0.002. The variant is not predicted to cause a splicing impact by by SpliceAI and VARSEAK, and the nucleotide is not conserved with a PhyloP score of -1.65 and a PhastCons score of ~0. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Thrombosis Variant Curation Expert Panel for SERPINC1: BA1, BP4, BP7. LINK:https://erepo.genome.network/evrepo/ui/classification/CA1251245/MONDO:0013144/084
Frequency
Consequence
ENST00000367698.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERPINC1 | NM_000488.4 | c.1218+27G>C | intron_variant | ENST00000367698.4 | NP_000479.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERPINC1 | ENST00000367698.4 | c.1218+27G>C | intron_variant | 1 | NM_000488.4 | ENSP00000356671 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0963 AC: 14643AN: 152024Hom.: 967 Cov.: 31
GnomAD3 exomes AF: 0.125 AC: 31403AN: 251440Hom.: 2339 AF XY: 0.130 AC XY: 17684AN XY: 135888
GnomAD4 exome AF: 0.120 AC: 170307AN: 1415278Hom.: 11170 Cov.: 24 AF XY: 0.123 AC XY: 86644AN XY: 706802
GnomAD4 genome AF: 0.0962 AC: 14640AN: 152142Hom.: 965 Cov.: 31 AF XY: 0.0964 AC XY: 7166AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hereditary antithrombin deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, reviewed by expert panel | curation | Clingen Thrombosis Variant Curation Expert Panel, ClinGen | Jul 25, 2023 | The NM_000488.4:c.1218+27G>C variant is reported at an Popmax FAF MAF of 0.2409 (4979/19948 alleles) in the East Asian population in the genomes in gnomAD v2.1.1 with a total of 2550 homozygotes, meeting BA1 criteria of FAF >= 0.002. The variant is not predicted to cause a splicing impact by by SpliceAI and VARSEAK, and the nucleotide is not conserved with a PhyloP score of -1.65 and a PhastCons score of ~0. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Thrombosis Variant Curation Expert Panel for SERPINC1: BA1, BP4, BP7. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at