rs879872

Variant names:

• chr11-256714-C-T
• rs879872

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0464 in 152,152 control chromosomes in the GnomAD database, including 622 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 0.046 (622 hom., cov: 31)
• Consequence: COX8BP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 publications found

Genes affected

COX8BP (HGNC:31395): (cytochrome c oxidase subunit 8B, pseudogene) Cytochrome c oxidase is the terminal enzyme of the mitochondrial respiratory chain. It is a multi-subunit enzyme complex that couples the transfer of electrons from cytochrome c to molecular oxygen and contributes to a proton electrochemical gradient across the inner mitochondrial membrane. The complex consists of 13 mitochondrial- and nuclear-encoded subunits. In addition a number of cytochrome c oxidase subunit pseudogenes have been found. This gene represents a subunit which has been inactivated by mutation and is nonfunctional in humans. [provided by RefSeq, Jul 2008]

ENSG00000293500 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COX8BP		n.256714C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293500	ENST00000688906.1	n.330+2673G>A		intron_variant	Intron 2 of 2
ENSG00000293500	ENST00000835501.1	n.495+2673G>A		intron_variant	Intron 2 of 2
ENSG00000293500	ENST00000835502.1	n.475+2673G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7051 AN: 152034 Hom.: 619 Cov.: 31

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0464 AC: 7055 AN: 152152 Hom.: 622 Cov.: 31 AF XY: 0.0500 AC XY: 3716 AN XY: 74372

African (AFR) AF: 0.0160 AC: 664 AN: 41526

American (AMR) AF: 0.0880 AC: 1346 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2196 AN: 5158

South Asian (SAS) AF: 0.0886 AC: 427 AN: 4818

European-Finnish (FIN) AF: 0.0248 AC: 262 AN: 10576

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0286 AC: 1943 AN: 67996

Other (OTH) AF: 0.0483 AC: 102 AN: 2112

Alfa AF: 0.0438 Hom.: 148

Bravo AF: 0.0536

Asia WGS AF: 0.225 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.15
DANN	Benign	0.71
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs879872; hg19: chr11-256714;