rs1311664031
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_001009944.3(PKD1):c.2200G>A(p.Gly734Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,237,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001009944.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.2200G>A | p.Gly734Ser | missense_variant | 11/46 | ENST00000262304.9 | NP_001009944.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.2200G>A | p.Gly734Ser | missense_variant | 11/46 | 1 | NM_001009944.3 | ENSP00000262304 | P5 | |
PKD1 | ENST00000423118.5 | c.2200G>A | p.Gly734Ser | missense_variant | 11/46 | 1 | ENSP00000399501 | A2 | ||
PKD1 | ENST00000488185.2 | c.472+2666G>A | intron_variant | 5 | ENSP00000456672 | |||||
PKD1 | ENST00000568591.5 | c.*528G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/12 | 2 | ENSP00000457162 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000497 AC: 6AN: 120686Hom.: 0 AF XY: 0.0000154 AC XY: 1AN XY: 64726
GnomAD4 exome AF: 0.0000212 AC: 23AN: 1085756Hom.: 0 Cov.: 16 AF XY: 0.0000183 AC XY: 10AN XY: 546810
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | Aug 25, 2016 | - - |
Polycystic kidney disease, adult type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at