7-130304559-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_016352.4(CPA4):c.466C>T(p.Arg156Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,611,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016352.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPA4 | NM_016352.4 | c.466C>T | p.Arg156Trp | missense_variant | Exon 5 of 11 | ENST00000222482.10 | NP_057436.2 | |
CPA4 | NM_001163446.2 | c.367C>T | p.Arg123Trp | missense_variant | Exon 4 of 10 | NP_001156918.1 | ||
CPA4 | XM_047420438.1 | c.154C>T | p.Arg52Trp | missense_variant | Exon 5 of 11 | XP_047276394.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251472Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135910
GnomAD4 exome AF: 0.000146 AC: 213AN: 1459366Hom.: 0 Cov.: 30 AF XY: 0.000146 AC XY: 106AN XY: 726194
GnomAD4 genome AF: 0.000138 AC: 21AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466C>T (p.R156W) alteration is located in exon 5 (coding exon 5) of the CPA4 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the arginine (R) at amino acid position 156 to be replaced by a tryptophan (W). 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