chr16-2093545-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM5
The NM_001009944.3(PKD1):c.11015G>T(p.Arg3672Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,597,364 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3672Q) has been classified as Likely benign.
Frequency
Consequence
NM_001009944.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.11015G>T | p.Arg3672Leu | missense_variant, splice_region_variant | 37/46 | ENST00000262304.9 | |
PKD1-AS1 | NR_135175.1 | n.303+533C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.11015G>T | p.Arg3672Leu | missense_variant, splice_region_variant | 37/46 | 1 | NM_001009944.3 | P5 | |
PKD1-AS1 | ENST00000563284.3 | n.194+533C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000134 AC: 3AN: 223828Hom.: 0 AF XY: 0.00000825 AC XY: 1AN XY: 121142
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1445072Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 717298
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at