2-97648394-C-T

Position:

• chr2-97648394-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.535 in 326,622 control chromosomes in the GnomAD database, including 52,926 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 0.48 (21230 hom., cov: 32)
  • Exomes 𝑓: 0.58 (31696 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

Genes affected

(HGNC:):

COX5B (HGNC:2269): (cytochrome c oxidase subunit 5B) Cytochrome C oxidase (COX) 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. The mitochondrially-encoded subunits perform the electron transfer and proton pumping activities. The functions of the nuclear-encoded subunits are unknown but they may play a role in the regulation and assembly of the complex. This gene encodes the nuclear-encoded subunit Vb of the human mitochondrial respiratory chain enzyme. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.97648394C>T		intergenic_region
COX5B	NM_001862.3	c.*286C>T		downstream_gene_variant		ENST00000258424.3	NP_001853.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COX5B	ENST00000258424.3	c.*286C>T		downstream_gene_variant		1	NM_001862.3	ENSP00000258424.2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73366 AN: 151950 Hom.: 21232 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.580 AC: 101249 AN: 174554 Hom.: 31696 Cov.: 2 AF XY: 0.571 AC XY: 50654 AN XY: 88780

Gnomad4 AFR exome AF: 0.204

Gnomad4 AMR exome AF: 0.421

Gnomad4 ASJ exome AF: 0.470

Gnomad4 EAS exome AF: 0.253

Gnomad4 SAS exome AF: 0.220

Gnomad4 FIN exome AF: 0.737

Gnomad4 NFE exome AF: 0.656

Gnomad4 OTH exome AF: 0.548

GnomAD4 genome AF: 0.482 AC: 73359 AN: 152068 Hom.: 21230 Cov.: 32 AF XY: 0.479 AC XY: 35569 AN XY: 74332

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.487

Alfa AF: 0.582 Hom.: 12622

Bravo AF: 0.453

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800649; hg19: chr2-98264857;