16-2112978-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001009944.3(PKD1):c.2986-15C>A 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 0.00001 in 1,595,686 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.2986-15C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000262304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.2986-15C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001009944.3 | P5 | |||
ENST00000568795.1 | n.161-69G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 239304Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130648
GnomAD4 exome AF: 0.00000485 AC: 7AN: 1443358Hom.: 0 Cov.: 33 AF XY: 0.00000557 AC XY: 4AN XY: 718614
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74478
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at