rs193921059
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014289.4(CAPN6):c.1757G>A(p.Arg586Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000021 in 1,095,510 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_014289.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN6 | NM_014289.4 | c.1757G>A | p.Arg586Gln | missense_variant | 13/13 | ENST00000324068.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN6 | ENST00000324068.2 | c.1757G>A | p.Arg586Gln | missense_variant | 13/13 | 1 | NM_014289.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 exomes AF: 0.0000224 AC: 4AN: 178613Hom.: 0 AF XY: 0.0000158 AC XY: 1AN XY: 63351
GnomAD4 exome AF: 0.0000210 AC: 23AN: 1095510Hom.: 0 Cov.: 29 AF XY: 0.0000194 AC XY: 7AN XY: 361028
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at