rs5907
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000185.4(SERPIND1):c.623G>A(p.Arg208His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,614,202 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R208C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000185.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPIND1 | NM_000185.4 | c.623G>A | p.Arg208His | missense_variant | 2/5 | ENST00000215727.10 | |
PI4KA | NM_058004.4 | c.2328+13258C>T | intron_variant | ENST00000255882.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPIND1 | ENST00000215727.10 | c.623G>A | p.Arg208His | missense_variant | 2/5 | 1 | NM_000185.4 | P1 | |
PI4KA | ENST00000255882.11 | c.2328+13258C>T | intron_variant | 1 | NM_058004.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00155 AC: 236AN: 152194Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00138 AC: 346AN: 251386Hom.: 0 AF XY: 0.00138 AC XY: 187AN XY: 135842
GnomAD4 exome AF: 0.00177 AC: 2593AN: 1461890Hom.: 3 Cov.: 31 AF XY: 0.00170 AC XY: 1236AN XY: 727244
GnomAD4 genome AF: 0.00155 AC: 236AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.00176 AC XY: 131AN XY: 74484
ClinVar
Submissions by phenotype
Heparin cofactor II deficiency Pathogenic:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 25, 1989 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at