chrX-77903028-G-GT

Position:

• chrX-77903028-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001866.3(COX7B):​c.165+276dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0098 (8 hom., 145 hem., cov: 20)
  • Exomes 𝑓: 0.21 (0 hom. 2 hem.)
• Consequence: COX7B NM_001866.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.963

Genes affected

COX7B (HGNC:2291): (cytochrome c oxidase subunit 7B) Cytochrome c oxidase (COX), the terminal component of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced cytochrome c to oxygen. This component is a heteromeric complex consisting of 3 catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits function in electron transfer, and the nuclear-encoded subunits may function in the regulation and assembly of the complex. This nuclear gene encodes subunit VIIb, which is highly similar to bovine COX VIIb protein and is found in all tissues. This gene may have several pseudogenes on chromosomes 1, 2, 20 and 22. [provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-77903028-G-GT is Benign according to our data. Variant chrX-77903028-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 1316365.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COX7B	NM_001866.3	c.165+276dupT		intron_variant		ENST00000650309.2	NP_001857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COX7B	ENST00000650309.2	c.165+276dupT		intron_variant			NM_001866.3	ENSP00000497474.1
COX7B	ENST00000475465.1	c.*258dupT		3_prime_UTR_variant	2/2	2		ENSP00000497958.1
COX7B	ENST00000373335.4	c.105+276dupT		intron_variant		2		ENSP00000496880.1
COX7B	ENST00000647835.1	c.*38+276dupT		intron_variant				ENSP00000497517.1

Frequencies

GnomAD3 genomes AF: 0.00980 AC: 884 AN: 90196 Hom.: 8 Cov.: 20 AF XY: 0.00642 AC XY: 145 AN XY: 22574

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00442

Gnomad ASJ AF: 0.00224

Gnomad EAS AF: 0.00307

Gnomad SAS AF: 0.00597

Gnomad FIN AF: 0.0239

Gnomad MID AF: 0.0199

Gnomad NFE AF: 0.00333

Gnomad OTH AF: 0.00844

GnomAD4 exome AF: 0.206 AC: 9855 AN: 47805 Hom.: 0 Cov.: 0 AF XY: 0.000323 AC XY: 2 AN XY: 6185

Gnomad4 AFR exome AF: 0.230

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.194

Gnomad4 EAS exome AF: 0.192

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.192

Gnomad4 NFE exome AF: 0.207

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.00980 AC: 884 AN: 90172 Hom.: 8 Cov.: 20 AF XY: 0.00642 AC XY: 145 AN XY: 22576

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.00442

Gnomad4 ASJ AF: 0.00224

Gnomad4 EAS AF: 0.00308

Gnomad4 SAS AF: 0.00602

Gnomad4 FIN AF: 0.0239

Gnomad4 NFE AF: 0.00333

Gnomad4 OTH AF: 0.00753

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs781818450; hg19: chrX-77158525;