16-2090553-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001009944.3(PKD1):āc.12176C>Gā(p.Ala4059Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,456,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. A4059V) has been classified as Benign.
Frequency
Consequence
NM_001009944.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.12176C>G | p.Ala4059Gly | missense_variant | 45/46 | ENST00000262304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.12176C>G | p.Ala4059Gly | missense_variant | 45/46 | 1 | NM_001009944.3 | P5 | |
PKD1 | ENST00000423118.5 | c.12173C>G | p.Ala4058Gly | missense_variant | 45/46 | 1 | A2 | ||
PKD1 | ENST00000472577.1 | n.204C>G | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000834 AC: 2AN: 239776Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 131122
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456948Hom.: 0 Cov.: 35 AF XY: 0.00000414 AC XY: 3AN XY: 724824
GnomAD4 genome Cov.: 34
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at