6-17426627-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006366.3(CAP2):c.159G>A(p.Met53Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,614,022 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006366.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAP2 | NM_006366.3 | c.159G>A | p.Met53Ile | missense_variant | 3/13 | ENST00000229922.7 | NP_006357.1 | |
CAP2 | NM_001363534.2 | c.159G>A | p.Met53Ile | missense_variant | 3/12 | NP_001350463.1 | ||
CAP2 | NM_001363533.2 | c.159G>A | p.Met53Ile | missense_variant | 3/10 | NP_001350462.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAP2 | ENST00000229922.7 | c.159G>A | p.Met53Ile | missense_variant | 3/13 | 1 | NM_006366.3 | ENSP00000229922.2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152126Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251480Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135916
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461778Hom.: 1 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727194
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152244Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2024 | The c.159G>A (p.M53I) alteration is located in exon 3 (coding exon 2) of the CAP2 gene. This alteration results from a G to A substitution at nucleotide position 159, causing the methionine (M) at amino acid position 53 to be replaced by an isoleucine (I). 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