14-24506065-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001836.5(CMA1):c.563G>T(p.Cys188Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,084 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_001836.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CMA1 | ENST00000250378.7 | c.563G>T | p.Cys188Phe | missense_variant | Exon 4 of 5 | 1 | NM_001836.5 | ENSP00000250378.3 | ||
CMA1 | ENST00000206446.4 | c.230G>T | p.Cys77Phe | missense_variant | Exon 3 of 4 | 1 | ENSP00000206446.4 | |||
ENSG00000258744 | ENST00000555109.1 | n.144-2069C>A | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 250996Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135630
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727228
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.563G>T (p.C188F) alteration is located in exon 4 (coding exon 4) of the CMA1 gene. This alteration results from a G to T substitution at nucleotide position 563, causing the cysteine (C) at amino acid position 188 to be replaced by a phenylalanine (F). 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