chr16-2114368-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001009944.3(PKD1):c.2655C>T(p.Cys885Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000685 in 1,609,636 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001009944.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.2655C>T | p.Cys885Cys | synonymous_variant | Exon 11 of 46 | ENST00000262304.9 | NP_001009944.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000703 AC: 107AN: 152156Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000949 AC: 233AN: 245394Hom.: 0 AF XY: 0.000933 AC XY: 125AN XY: 134038
GnomAD4 exome AF: 0.000683 AC: 996AN: 1457362Hom.: 2 Cov.: 34 AF XY: 0.000701 AC XY: 508AN XY: 725032
GnomAD4 genome AF: 0.000696 AC: 106AN: 152274Hom.: 1 Cov.: 32 AF XY: 0.000699 AC XY: 52AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
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PKD1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at