rs756792624
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_138694.4(PKHD1):c.10319T>A(p.Val3440Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,534 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V3440V) has been classified as Likely benign.
Frequency
Consequence
NM_138694.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.10319T>A | p.Val3440Asp | missense_variant | 61/67 | ENST00000371117.8 | |
LOC124900615 | XR_926871.3 | n.155+7434A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.10319T>A | p.Val3440Asp | missense_variant | 61/67 | 1 | NM_138694.4 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250950Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135622
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461534Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727094
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive polycystic kidney disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 12, 2018 | - - |
Autosomal dominant polycystic liver disease Benign:1
Likely benign, no assertion criteria provided | research | Laboratory of Gastroenterology and Hepatology, Radboud University Medical Center | Sep 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at