19-5914606-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004058.5(CAPS):c.127G>A(p.Ala43Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,613,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004058.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPS | NM_004058.5 | c.127G>A | p.Ala43Thr | missense_variant | 3/5 | ENST00000588776.8 | NP_004049.3 | |
CAPS | NM_080590.4 | c.127G>A | p.Ala43Thr | missense_variant | 3/5 | NP_542157.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPS | ENST00000588776.8 | c.127G>A | p.Ala43Thr | missense_variant | 3/5 | 1 | NM_004058.5 | ENSP00000465883.2 | ||
ENSG00000267314 | ENST00000588891.1 | n.*222G>A | non_coding_transcript_exon_variant | 4/4 | 4 | ENSP00000468419.1 | ||||
ENSG00000267314 | ENST00000588891.1 | n.*222G>A | 3_prime_UTR_variant | 4/4 | 4 | ENSP00000468419.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250430Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135480
GnomAD4 exome AF: 0.000130 AC: 190AN: 1461032Hom.: 0 Cov.: 33 AF XY: 0.000127 AC XY: 92AN XY: 726762
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.127G>A (p.A43T) alteration is located in exon 3 (coding exon 2) of the CAPS gene. This alteration results from a G to A substitution at nucleotide position 127, causing the alanine (A) at amino acid position 43 to be replaced by a threonine (T). 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