4-46889893-A-G

Position:

• chr4-46889893-A-G

Variant summary

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

The NM_130902.3(COX7B2):​c.-105+19267T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 150,182 control chromosomes in the GnomAD database, including 20,567 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 0.52 (20567 hom., cov: 29)
• Consequence: COX7B2 NM_130902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

COX7B2 (HGNC:24381): (cytochrome c oxidase subunit 7B2) Predicted to enable cytochrome-c oxidase activity. Predicted to be involved in electron transport chain; oxidative phosphorylation; and proton transmembrane transport. Predicted to be located in mitochondrial respirasome. Predicted to be integral component of membrane. Predicted to be part of respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COX7B2	NM_130902.3	c.-105+19267T>C		intron_variant		ENST00000355591.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COX7B2	ENST00000355591.8	c.-105+19267T>C		intron_variant		1	NM_130902.3	P4
COX7B2	ENST00000396533.5	c.-203-13156T>C		intron_variant		1		P4
COX7B2	ENST00000505102.1	c.-105+13983T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.521 AC: 78183 AN: 150086 Hom.: 20539 Cov.: 29

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.521 AC: 78258 AN: 150182 Hom.: 20567 Cov.: 29 AF XY: 0.521 AC XY: 38143 AN XY: 73216

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.503

Alfa AF: 0.515 Hom.: 2374

Bravo AF: 0.521

Asia WGS AF: 0.585 AC: 2007 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6811055; hg19: chr4-46891910;