chr16-2089717-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_001009944.3(PKD1):c.*10C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000153 in 1,573,260 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001009944.3 3_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.*10C>T | 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.*10C>T | 3_prime_UTR_variant | Exon 46 of 46 | 1 | NM_001009944.3 | ENSP00000262304.4 | |||
PKD1 | ENST00000423118 | c.*10C>T | 3_prime_UTR_variant | Exon 46 of 46 | 1 | ENSP00000399501.1 | ||||
PKD1 | ENST00000472577.1 | n.950C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152284Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182928Hom.: 0 AF XY: 0.0000101 AC XY: 1AN XY: 99194
GnomAD4 exome AF: 0.0000155 AC: 22AN: 1420976Hom.: 0 Cov.: 31 AF XY: 0.0000142 AC XY: 10AN XY: 702856
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152284Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74402
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at