NM_032330.3:c.178C>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032330.3(CAPNS2):c.178C>T(p.Pro60Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000911 in 1,613,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPNS2 | NM_032330.3 | c.178C>T | p.Pro60Ser | missense_variant | Exon 1 of 1 | ENST00000457326.3 | NP_115706.1 | |
LPCAT2 | NM_017839.5 | c.1216-7697C>T | intron_variant | Intron 11 of 13 | ENST00000262134.10 | NP_060309.2 | ||
LPCAT2 | XM_047434277.1 | c.1048-7697C>T | intron_variant | Intron 11 of 13 | XP_047290233.1 | |||
LPCAT2 | XM_011523169.4 | c.406-7697C>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.178C>T | p.Pro60Ser | missense_variant | Exon 1 of 1 | 6 | NM_032330.3 | ENSP00000400882.2 | ||
LPCAT2 | ENST00000262134.10 | c.1216-7697C>T | intron_variant | Intron 11 of 13 | 1 | NM_017839.5 | ENSP00000262134.5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248822Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134974
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461600Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 727074
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74408
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.178C>T (p.P60S) 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 178, causing the proline (P) at amino acid position 60 to be replaced by a serine (S). 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