rs203710
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_006505.5(PVR):c.1020G>A(p.Met340Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.021 in 1,611,156 control chromosomes in the GnomAD database, including 435 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006505.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.1020G>A | p.Met340Ile | missense_variant | 6/8 | ENST00000425690.8 | |
PVR | NM_001135770.4 | c.1020G>A | p.Met340Ile | missense_variant | 6/6 | ||
PVR | NM_001135768.3 | c.1015+5G>A | splice_donor_5th_base_variant, intron_variant | ||||
PVR | NM_001135769.3 | c.991+860G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PVR | ENST00000425690.8 | c.1020G>A | p.Met340Ile | missense_variant | 6/8 | 1 | NM_006505.5 | P2 | |
CEACAM16-AS1 | ENST00000662585.1 | n.476-26151C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0138 AC: 2102AN: 152196Hom.: 26 Cov.: 32
GnomAD4 exome AF: 0.0217 AC: 31693AN: 1458842Hom.: 409 Cov.: 30 AF XY: 0.0213 AC XY: 15453AN XY: 725976
GnomAD4 genome ? AF: 0.0138 AC: 2102AN: 152314Hom.: 26 Cov.: 32 AF XY: 0.0125 AC XY: 930AN XY: 74498
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at