rs11083846
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016457.5(PRKD2):c.667-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,613,770 control chromosomes in the GnomAD database, including 36,625 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_016457.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKD2 | NM_016457.5 | c.667-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000291281.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKD2 | ENST00000291281.9 | c.667-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016457.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24468AN: 152080Hom.: 2420 Cov.: 32
GnomAD3 exomes AF: 0.173 AC: 43299AN: 250810Hom.: 4475 AF XY: 0.179 AC XY: 24209AN XY: 135544
GnomAD4 exome AF: 0.209 AC: 305914AN: 1461572Hom.: 34205 Cov.: 36 AF XY: 0.209 AC XY: 152133AN XY: 727064
GnomAD4 genome ? AF: 0.161 AC: 24470AN: 152198Hom.: 2420 Cov.: 32 AF XY: 0.159 AC XY: 11829AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 30, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at