rs714948
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006505.5(PVR):c.*834A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,318 control chromosomes in the GnomAD database, including 65,482 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.93 ( 65427 hom., cov: 31)
Exomes 𝑓: 0.94 ( 55 hom. )
Consequence
PVR
NM_006505.5 3_prime_UTR
NM_006505.5 3_prime_UTR
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0640
Genes affected
PVR (HGNC:9705): (PVR cell adhesion molecule) The protein encoded by this gene is a transmembrane glycoprotein belonging to the immunoglobulin superfamily. The external domain mediates cell attachment to the extracellular matrix molecule vitronectin, while its intracellular domain interacts with the dynein light chain Tctex-1/DYNLT1. The gene is specific to the primate lineage, and serves as a cellular receptor for poliovirus in the first step of poliovirus replication. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.*834A>C | 3_prime_UTR_variant | 8/8 | ENST00000425690.8 | ||
PVR | NM_001135768.3 | c.*834A>C | 3_prime_UTR_variant | 8/8 | |||
PVR | NM_001135769.3 | c.*834A>C | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PVR | ENST00000425690.8 | c.*834A>C | 3_prime_UTR_variant | 8/8 | 1 | NM_006505.5 | P2 | ||
CEACAM16-AS1 | ENST00000662585.1 | n.476-30026T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.926 AC: 140828AN: 152074Hom.: 65371 Cov.: 31
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GnomAD4 exome AF: 0.937 AC: 118AN: 126Hom.: 55 Cov.: 0 AF XY: 0.947 AC XY: 89AN XY: 94
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GnomAD4 genome ? AF: 0.926 AC: 140942AN: 152192Hom.: 65427 Cov.: 31 AF XY: 0.927 AC XY: 68989AN XY: 74398
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at