chr15-74937999-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004255.4(COX5A):c.16C>T(p.Leu6Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000603 in 1,231,986 control chromosomes in the GnomAD database, including 1 homozygotes. 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 | UniProt |
---|---|---|---|---|---|---|---|
COX5A | NM_004255.4 | c.16C>T | p.Leu6Phe | missense_variant | 1/5 | ENST00000322347.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COX5A | ENST00000322347.11 | c.16C>T | p.Leu6Phe | missense_variant | 1/5 | 1 | NM_004255.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000421 AC: 64AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000555 AC: 1AN: 1802Hom.: 0 AF XY: 0.000936 AC XY: 1AN XY: 1068
GnomAD4 exome AF: 0.000629 AC: 679AN: 1079722Hom.: 1 Cov.: 30 AF XY: 0.000637 AC XY: 325AN XY: 510412
GnomAD4 genome ? AF: 0.000420 AC: 64AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.16C>T (p.L6F) alteration is located in exon 1 (coding exon 1) of the COX5A gene. This alteration results from a C to T substitution at nucleotide position 16, causing the leucine (L) at amino acid position 6 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