19-44649897-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_006505.5(PVR):c.516C>T(p.Arg172Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006505.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.516C>T | p.Arg172Arg | synonymous_variant | Exon 3 of 8 | ENST00000425690.8 | NP_006496.4 | |
PVR | NM_001135770.4 | c.516C>T | p.Arg172Arg | synonymous_variant | Exon 3 of 6 | NP_001129242.2 | ||
PVR | NM_001135768.3 | c.516C>T | p.Arg172Arg | synonymous_variant | Exon 3 of 8 | NP_001129240.1 | ||
PVR | NM_001135769.3 | c.516C>T | p.Arg172Arg | synonymous_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.516C>T | p.Arg172Arg | synonymous_variant | Exon 3 of 8 | 1 | NM_006505.5 | ENSP00000402060.2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152176Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249354Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134934
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461548Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727044
GnomAD4 genome AF: 0.000105 AC: 16AN: 152294Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 8AN XY: 74472
ClinVar
Submissions by phenotype
PVR-related disorder Benign:1
This variant is classified as likely 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