chr19-44650057-G-A
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_006505.5(PVR):c.676G>A(p.Glu226Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000784 in 1,554,248 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_006505.5 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.676G>A | p.Glu226Lys | missense_variant | Exon 3 of 8 | ENST00000425690.8 | NP_006496.4 | |
PVR | NM_001135770.4 | c.676G>A | p.Glu226Lys | missense_variant | Exon 3 of 6 | NP_001129242.2 | ||
PVR | NM_001135768.3 | c.676G>A | p.Glu226Lys | missense_variant | Exon 3 of 8 | NP_001129240.1 | ||
PVR | NM_001135769.3 | c.676G>A | p.Glu226Lys | missense_variant | Exon 3 of 7 | NP_001129241.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PVR | ENST00000425690.8 | c.676G>A | p.Glu226Lys | missense_variant | Exon 3 of 8 | 1 | NM_006505.5 | ENSP00000402060.2 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 183AN: 152190Hom.: 2 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.00285 AC: 571AN: 200178 AF XY: 0.00250 show subpopulations
GnomAD4 exome AF: 0.000739 AC: 1036AN: 1401940Hom.: 16 Cov.: 31 AF XY: 0.000730 AC XY: 504AN XY: 690746 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00120 AC: 183AN: 152308Hom.: 2 Cov.: 31 AF XY: 0.00146 AC XY: 109AN XY: 74474 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
PVR-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at