4-46889893-A-G

Variant names:

• chr4-46889893-A-G
• rs6811055
• NM_130902.3:c.-105+19267T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ENSG00000299086 (HGNC:58780):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130902.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX7B2	NM_130902.3	MANE Select	c.-105+19267T>C		intron	N/A	NP_570972.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX7B2	ENST00000355591.8	TSL:1 MANE Select	c.-105+19267T>C		intron	N/A	ENSP00000347799.3
	COX7B2	ENST00000396533.5	TSL:1	c.-203-13156T>C		intron	N/A	ENSP00000379784.1
	COX7B2	ENST00000505102.1	TSL:3	c.-105+13983T>C		intron	N/A	ENSP00000423519.1

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

African (AFR) AF: 0.476 AC: 19512 AN: 41004

American (AMR) AF: 0.568 AC: 8585 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1604 AN: 3464

East Asian (EAS) AF: 0.666 AC: 3421 AN: 5134

South Asian (SAS) AF: 0.550 AC: 2616 AN: 4754

European-Finnish (FIN) AF: 0.545 AC: 5361 AN: 9838

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.526 AC: 35560 AN: 67602

Other (OTH) AF: 0.503 AC: 1045 AN: 2078

Alfa AF: 0.513 Hom.: 2449

Bravo AF: 0.521

Asia WGS AF: 0.585 AC: 2007 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.53
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6811055; hg19: chr4-46891910;