rs12933806
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000525539.5(PKD1L2):c.547G>T(p.Val183Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,608,694 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 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
ENST00000525539.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1L2 | NR_126532.3 | n.571G>T | non_coding_transcript_exon_variant | 3/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD1L2 | ENST00000525539.5 | c.547G>T | p.Val183Phe | missense_variant | 3/43 | 1 | ENSP00000434417 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151994Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000206 AC: 49AN: 237516Hom.: 1 AF XY: 0.000302 AC XY: 39AN XY: 129208
GnomAD4 exome AF: 0.000105 AC: 153AN: 1456582Hom.: 6 Cov.: 33 AF XY: 0.000170 AC XY: 123AN XY: 724122
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152112Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at