rs1441482246
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM1BS2_Supporting
The ENST00000262304.9(PKD1):c.461C>T(p.Thr154Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,311,582 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T154T) has been classified as Likely benign.
Frequency
Consequence
ENST00000262304.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.461C>T | p.Thr154Met | missense_variant | 4/46 | ENST00000262304.9 | NP_001009944.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.461C>T | p.Thr154Met | missense_variant | 4/46 | 1 | NM_001009944.3 | ENSP00000262304 | P5 | |
PKD1 | ENST00000423118.5 | c.461C>T | p.Thr154Met | missense_variant | 4/46 | 1 | ENSP00000399501 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000286 AC: 2AN: 69988Hom.: 0 AF XY: 0.0000281 AC XY: 1AN XY: 35588
GnomAD4 exome AF: 0.0000130 AC: 17AN: 1311582Hom.: 0 Cov.: 19 AF XY: 0.0000122 AC XY: 8AN XY: 656536
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 23, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at