rs777300399
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032330.3(CAPNS2):c.170C>A(p.Thr57Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T57I) has been classified as Uncertain significance.
Frequency
Consequence
NM_032330.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPNS2 | NM_032330.3 | c.170C>A | p.Thr57Asn | missense_variant | Exon 1 of 1 | ENST00000457326.3 | NP_115706.1 | |
LPCAT2 | NM_017839.5 | c.1216-7705C>A | intron_variant | Intron 11 of 13 | ENST00000262134.10 | NP_060309.2 | ||
LPCAT2 | XM_047434277.1 | c.1048-7705C>A | intron_variant | Intron 11 of 13 | XP_047290233.1 | |||
LPCAT2 | XM_011523169.4 | c.406-7705C>A | 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.170C>A | p.Thr57Asn | missense_variant | Exon 1 of 1 | 6 | NM_032330.3 | ENSP00000400882.2 | ||
LPCAT2 | ENST00000262134.10 | c.1216-7705C>A | intron_variant | Intron 11 of 13 | 1 | NM_017839.5 | ENSP00000262134.5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248834Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134980
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1AN: 1461592Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727070
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at