1-112647213-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006135.3(CAPZA1):c.43C>T(p.Arg15Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000152 in 1,510,422 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006135.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPZA1 | NM_006135.3 | c.43C>T | p.Arg15Cys | missense_variant | Exon 2 of 10 | ENST00000263168.4 | NP_006126.1 | |
CAPZA1 | XM_017002424.3 | c.43C>T | p.Arg15Cys | missense_variant | Exon 2 of 10 | XP_016857913.1 | ||
CAPZA1 | XM_011542225.4 | c.43C>T | p.Arg15Cys | missense_variant | Exon 2 of 9 | XP_011540527.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPZA1 | ENST00000263168.4 | c.43C>T | p.Arg15Cys | missense_variant | Exon 2 of 10 | 1 | NM_006135.3 | ENSP00000263168.3 | ||
CAPZA1 | ENST00000476936.5 | n.69C>T | non_coding_transcript_exon_variant | Exon 2 of 8 | 3 | |||||
CAPZA1 | ENST00000485542.5 | n.83C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
CAPZA1 | ENST00000498626.1 | n.96C>T | non_coding_transcript_exon_variant | Exon 3 of 9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000309 AC: 7AN: 226624Hom.: 0 AF XY: 0.0000243 AC XY: 3AN XY: 123222
GnomAD4 exome AF: 0.0000147 AC: 20AN: 1358364Hom.: 0 Cov.: 25 AF XY: 0.0000119 AC XY: 8AN XY: 673924
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.43C>T (p.R15C) alteration is located in exon 2 (coding exon 2) of the CAPZA1 gene. This alteration results from a C to T substitution at nucleotide position 43, causing the arginine (R) at amino acid position 15 to be replaced by a cysteine (C). 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