rs2069936
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001375607.1(PROC):c.14G>A(p.Arg5Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000055 in 1,289,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001375607.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000204 AC: 28AN: 137018Hom.: 0 AF XY: 0.000175 AC XY: 13AN XY: 74396
GnomAD4 exome AF: 0.0000519 AC: 59AN: 1137506Hom.: 0 Cov.: 29 AF XY: 0.0000538 AC XY: 30AN XY: 558054
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74464
ClinVar
Submissions by phenotype
Thrombophilia due to protein C deficiency, autosomal dominant Uncertain:1Benign:1
- -
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at