rs17598636

Variant names:

• chr4-46851197-T-C
• rs17598636
• NM_130902.3:c.-104-6183A>G

Variant summary

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

The NM_130902.3(COX7B2):​c.-104-6183A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0566 in 152,076 control chromosomes in the GnomAD database, including 312 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 0.057 (312 hom., cov: 32)
• Consequence: COX7B2 NM_130902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 5 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 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.-104-6183A>G		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.-104-6183A>G		intron	N/A	ENSP00000347799.3
	COX7B2	ENST00000396533.5	TSL:1	c.-104-6183A>G		intron	N/A	ENSP00000379784.1
	COX7B2	ENST00000543208.5	TSL:5	c.-107-6183A>G		intron	N/A	ENSP00000437439.1

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8613 AN: 151958 Hom.: 314 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0505

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0999

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0566 AC: 8612 AN: 152076 Hom.: 312 Cov.: 32 AF XY: 0.0580 AC XY: 4314 AN XY: 74322

African (AFR) AF: 0.0361 AC: 1500 AN: 41540

American (AMR) AF: 0.0503 AC: 767 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.0997 AC: 514 AN: 5154

South Asian (SAS) AF: 0.162 AC: 777 AN: 4804

European-Finnish (FIN) AF: 0.0367 AC: 389 AN: 10610

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0608 AC: 4131 AN: 67946

Other (OTH) AF: 0.0720 AC: 152 AN: 2112

Alfa AF: 0.0645 Hom.: 297

Bravo AF: 0.0537

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.46
PhyloP100		0.49
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: rs17598636; hg19: chr4-46853214;