rs2452505
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032439.4(PHYHIPL):āc.1024G>Cā(p.Val342Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 1,613,906 control chromosomes in the GnomAD database, including 552,085 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_032439.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHYHIPL | ENST00000373880.9 | c.1024G>C | p.Val342Leu | missense_variant | 5/5 | 1 | NM_032439.4 | ENSP00000362987.4 | ||
PHYHIPL | ENST00000373878.3 | c.946G>C | p.Val316Leu | missense_variant | 5/5 | 1 | ENSP00000362985.3 | |||
PHYHIPL | ENST00000486074.2 | n.*965G>C | non_coding_transcript_exon_variant | 6/6 | 2 | ENSP00000423634.1 | ||||
PHYHIPL | ENST00000486074.2 | n.*965G>C | 3_prime_UTR_variant | 6/6 | 2 | ENSP00000423634.1 |
Frequencies
GnomAD3 genomes AF: 0.761 AC: 115714AN: 151980Hom.: 45755 Cov.: 32
GnomAD3 exomes AF: 0.820 AC: 205687AN: 250832Hom.: 85505 AF XY: 0.819 AC XY: 110984AN XY: 135558
GnomAD4 exome AF: 0.830 AC: 1212985AN: 1461808Hom.: 506323 Cov.: 61 AF XY: 0.827 AC XY: 601679AN XY: 727204
GnomAD4 genome AF: 0.761 AC: 115751AN: 152098Hom.: 45762 Cov.: 32 AF XY: 0.765 AC XY: 56912AN XY: 74364
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at