16-2089719-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BS2_Supporting
The NM_001009944.3(PKD1):c.*8T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,575,044 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 Likely benign (no stars).
Frequency
Consequence
NM_001009944.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.*8T>G | 3_prime_UTR_variant | Exon 46 of 46 | ENST00000262304.9 | NP_001009944.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304 | c.*8T>G | 3_prime_UTR_variant | Exon 46 of 46 | 1 | NM_001009944.3 | ENSP00000262304.4 | |||
PKD1 | ENST00000423118 | c.*8T>G | 3_prime_UTR_variant | Exon 46 of 46 | 1 | ENSP00000399501.1 | ||||
PKD1 | ENST00000472577.1 | n.948T>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000119 AC: 22AN: 185122Hom.: 0 AF XY: 0.000149 AC XY: 15AN XY: 100482
GnomAD4 exome AF: 0.000112 AC: 160AN: 1422796Hom.: 0 Cov.: 31 AF XY: 0.000126 AC XY: 89AN XY: 703952
GnomAD4 genome AF: 0.000164 AC: 25AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.000161 AC XY: 12AN XY: 74392
ClinVar
Submissions by phenotype
PKD1-related disorder Benign:1
This variant is classified as likely 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