19-44647486-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006505.5(PVR):c.343G>C(p.Val115Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006505.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.343G>C | p.Val115Leu | missense_variant | 2/8 | ENST00000425690.8 | |
PVR | NM_001135770.4 | c.343G>C | p.Val115Leu | missense_variant | 2/6 | ||
PVR | NM_001135768.3 | c.343G>C | p.Val115Leu | missense_variant | 2/8 | ||
PVR | NM_001135769.3 | c.343G>C | p.Val115Leu | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PVR | ENST00000425690.8 | c.343G>C | p.Val115Leu | missense_variant | 2/8 | 1 | NM_006505.5 | P2 | |
CEACAM16-AS1 | ENST00000662585.1 | n.476-14867C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248810Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134750
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461830Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727214
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The c.343G>C (p.V115L) alteration is located in exon 2 (coding exon 2) of the PVR gene. This alteration results from a G to C substitution at nucleotide position 343, causing the valine (V) at amino acid position 115 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at