rs1130474
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004374.4(COX6C):c.-28A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,522,390 control chromosomes in the GnomAD database, including 30,101 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.24 ( 5682 hom., cov: 32)
Exomes 𝑓: 0.18 ( 24419 hom. )
Consequence
COX6C
NM_004374.4 5_prime_UTR
NM_004374.4 5_prime_UTR
Scores
2
Splicing: ADA: 0.00002058
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.59
Genes affected
COX6C (HGNC:2285): (cytochrome c oxidase subunit 6C) Cytochrome c oxidase, the terminal enzyme of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced cytochrome c to oxygen. It is a heteromeric complex consisting of 3 catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits function in electron transfer, and the nuclear-encoded subunits may be involved in the regulation and assembly of the complex. This nuclear gene encodes subunit VIc, which has 77% amino acid sequence identity with mouse subunit VIc. This gene is up-regulated in prostate cancer cells. A pseudogene has been found on chromosomes 16p12. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX6C | NM_004374.4 | c.-28A>G | 5_prime_UTR_variant | 2/4 | ENST00000520468.7 | ||
COX6C | XM_017013020.2 | c.-28A>G | 5_prime_UTR_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COX6C | ENST00000520468.7 | c.-28A>G | 5_prime_UTR_variant | 2/4 | 1 | NM_004374.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.245 AC: 37213AN: 152060Hom.: 5662 Cov.: 32
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GnomAD3 exomes AF: 0.185 AC: 41837AN: 225632Hom.: 4518 AF XY: 0.180 AC XY: 22071AN XY: 122528
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GnomAD4 exome AF: 0.181 AC: 248313AN: 1370212Hom.: 24419 Cov.: 21 AF XY: 0.179 AC XY: 122740AN XY: 684746
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GnomAD4 genome ? AF: 0.245 AC: 37266AN: 152178Hom.: 5682 Cov.: 32 AF XY: 0.240 AC XY: 17889AN XY: 74422
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at