chr15-74937921-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004255.4(COX5A):c.94G>A(p.Ala32Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000203 in 1,231,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004255.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COX5A | NM_004255.4 | c.94G>A | p.Ala32Thr | missense_variant | 1/5 | ENST00000322347.11 | NP_004246.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COX5A | ENST00000322347.11 | c.94G>A | p.Ala32Thr | missense_variant | 1/5 | 1 | NM_004255.4 | ENSP00000317780.6 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152130Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000148 AC: 16AN: 1079712Hom.: 0 Cov.: 30 AF XY: 0.0000255 AC XY: 13AN XY: 510092
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.94G>A (p.A32T) alteration is located in exon 1 (coding exon 1) of the COX5A gene. This alteration results from a G to A substitution at nucleotide position 94, causing the alanine (A) at amino acid position 32 to be replaced by a threonine (T). 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