7-130305844-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016352.4(CPA4):c.515C>T(p.Pro172Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPA4 | NM_016352.4 | c.515C>T | p.Pro172Leu | missense_variant | Exon 6 of 11 | ENST00000222482.10 | NP_057436.2 | |
CPA4 | NM_001163446.2 | c.416C>T | p.Pro139Leu | missense_variant | Exon 5 of 10 | NP_001156918.1 | ||
CPA4 | XM_047420438.1 | c.203C>T | p.Pro68Leu | missense_variant | Exon 6 of 11 | XP_047276394.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251402Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135890
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461836Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 727224
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.515C>T (p.P172L) alteration is located in exon 6 (coding exon 6) of the CPA4 gene. This alteration results from a C to T substitution at nucleotide position 515, causing the proline (P) at amino acid position 172 to be replaced by a leucine (L). 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