16-55567342-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_032330.3(CAPNS2):c.586C>T(p.Arg196Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032330.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPNS2 | NM_032330.3 | c.586C>T | p.Arg196Trp | missense_variant | Exon 1 of 1 | ENST00000457326.3 | NP_115706.1 | |
LPCAT2 | NM_017839.5 | c.1216-7289C>T | intron_variant | Intron 11 of 13 | ENST00000262134.10 | NP_060309.2 | ||
LPCAT2 | XM_047434277.1 | c.1048-7289C>T | intron_variant | Intron 11 of 13 | XP_047290233.1 | |||
LPCAT2 | XM_011523169.4 | c.406-7289C>T | intron_variant | Intron 8 of 10 | XP_011521471.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPNS2 | ENST00000457326.3 | c.586C>T | p.Arg196Trp | missense_variant | Exon 1 of 1 | 6 | NM_032330.3 | ENSP00000400882.2 | ||
LPCAT2 | ENST00000262134.10 | c.1216-7289C>T | intron_variant | Intron 11 of 13 | 1 | NM_017839.5 | ENSP00000262134.5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 245526Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133438
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461374Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726956
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.586C>T (p.R196W) alteration is located in exon 1 (coding exon 1) of the CAPNS2 gene. This alteration results from a C to T substitution at nucleotide position 586, causing the arginine (R) at amino acid position 196 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at