rs200930978
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM5BP4BS2
The NM_001009944.3(PKD1):c.6224G>A(p.Arg2075His) variant causes a missense change. The variant allele was found at a frequency of 0.000331 in 1,604,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2075L) has been classified 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.6224G>A | p.Arg2075His | missense_variant | 15/46 | ENST00000262304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.6224G>A | p.Arg2075His | missense_variant | 15/46 | 1 | NM_001009944.3 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000817 AC: 19AN: 232582Hom.: 0 AF XY: 0.0000938 AC XY: 12AN XY: 127908
GnomAD4 exome AF: 0.000352 AC: 511AN: 1452684Hom.: 0 Cov.: 34 AF XY: 0.000352 AC XY: 254AN XY: 722290
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74386
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at