rs11540085
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_006505.5(PVR):c.-1C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 1,514,500 control chromosomes in the GnomAD database, including 334 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 5_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000425690.8 | NP_006496.4 | ||
PVR | NM_001135770.4 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 6 | NP_001129242.2 | |||
PVR | NM_001135768.3 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 8 | NP_001129240.1 | |||
PVR | NM_001135769.3 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 7 | NP_001129241.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PVR | ENST00000425690 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_006505.5 | ENSP00000402060.2 |
Frequencies
GnomAD3 genomes AF: 0.0124 AC: 1887AN: 152188Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.0118 AC: 1296AN: 110010Hom.: 19 AF XY: 0.0118 AC XY: 716AN XY: 60688
GnomAD4 exome AF: 0.0194 AC: 26420AN: 1362194Hom.: 315 Cov.: 31 AF XY: 0.0188 AC XY: 12628AN XY: 672096
GnomAD4 genome AF: 0.0124 AC: 1887AN: 152306Hom.: 19 Cov.: 32 AF XY: 0.0118 AC XY: 879AN XY: 74468
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