rs763213387
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM1BP4_StrongBS2_Supporting
The NM_001009944.3(PKD1):āc.1894A>Gā(p.Asn632Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000627 in 1,594,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_001009944.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.1894A>G | p.Asn632Asp | missense_variant | 10/46 | ENST00000262304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.1894A>G | p.Asn632Asp | missense_variant | 10/46 | 1 | NM_001009944.3 | P5 | |
PKD1 | ENST00000423118.5 | c.1894A>G | p.Asn632Asp | missense_variant | 10/46 | 1 | A2 | ||
PKD1 | ENST00000488185.2 | c.472+1908A>G | intron_variant | 5 | |||||
PKD1 | ENST00000568591.5 | c.*222A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152056Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000416 AC: 6AN: 1442606Hom.: 0 Cov.: 32 AF XY: 0.00000279 AC XY: 2AN XY: 717348
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74404
ClinVar
Submissions by phenotype
Polycystic kidney disease, adult type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 11, 2022 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 11, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at