16-2091607-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001009944.3(PKD1):c.11538-10C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000142 in 1,408,954 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 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.11538-10C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000262304.9 | |||
PKD1-AS1 | NR_135175.1 | n.172G>C | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.11538-10C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001009944.3 | P5 | |||
PKD1-AS1 | ENST00000563284.3 | n.69G>C | splice_region_variant, non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000116 AC: 2AN: 172080Hom.: 0 AF XY: 0.0000104 AC XY: 1AN XY: 95814
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1408954Hom.: 0 Cov.: 32 AF XY: 0.00000143 AC XY: 1AN XY: 697572
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at