rs763243200
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_138370.3(PKDCC):c.639+1G>A variant causes a splice donor change. The variant allele was found at a frequency of 0.00000343 in 1,457,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_138370.3 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKDCC | NM_138370.3 | c.639+1G>A | splice_donor_variant | ENST00000294964.6 | NP_612379.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKDCC | ENST00000294964.6 | c.639+1G>A | splice_donor_variant | 1 | NM_138370.3 | ENSP00000294964 | P1 | |||
PKDCC | ENST00000401498.6 | c.497+1G>A | splice_donor_variant, NMD_transcript_variant | 5 | ENSP00000385220 | |||||
PKDCC | ENST00000485578.1 | n.260+1G>A | splice_donor_variant, non_coding_transcript_variant | 2 | ||||||
PKDCC | ENST00000492861.1 | n.65+1G>A | splice_donor_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000306 AC: 4AN: 1305406Hom.: 0 Cov.: 33 AF XY: 0.00000312 AC XY: 2AN XY: 640114
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at