rs143521873
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_000488.4(SERPINC1):c.529C>T(p.Arg177Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R177H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000488.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINC1 | NM_000488.4 | c.529C>T | p.Arg177Cys | missense_variant | 3/7 | ENST00000367698.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINC1 | ENST00000367698.4 | c.529C>T | p.Arg177Cys | missense_variant | 3/7 | 1 | NM_000488.4 | P1 | |
SERPINC1 | ENST00000487183.1 | n.234C>T | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000539 AC: 82AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251482Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135916
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461864Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727240
GnomAD4 genome ? AF: 0.000539 AC: 82AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000538 AC XY: 40AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Aug 02, 2023 | PP3 - |
Hereditary antithrombin deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at