1-234374112-GT-G

Position:

• chr1-234374112-GT-G

Variant summary

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

The NM_001301733.1(COA6):​c.-117delT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.59 (25165 hom., cov: 0)
  • Exomes 𝑓: 0.53 (70628 hom.)
• Consequence: COA6 NM_001301733.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0550

Genes affected

COA6 (HGNC:18025): (cytochrome c oxidase assembly factor 6) This gene encodes a member of the cytochrome c oxidase subunit 6B family. The encoded protein associates with cytochrome c oxidase may act has an cytochrome c oxidase mitochondrial respiratory complex VI assembly factor. Mutations in this gene may be associated with fatal infantile cardiomyopathy. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-234374112-GT-G is Benign according to our data. Variant chr1-234374112-GT-G is described in ClinVar as [Benign]. Clinvar id is 1248350.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COA6	NM_001206641.3	c.213-101delT		intron_variant		ENST00000366615.10	NP_001193570.2
COA6	NM_001301733.1	c.-117delT		5_prime_UTR_variant	1/2		NP_001288662.1
COA6	NM_001012985.2	c.123-101delT		intron_variant			NP_001013003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COA6	ENST00000366612	c.-117delT		5_prime_UTR_variant	1/2	1		ENSP00000355571.1
COA6	ENST00000366615.10	c.213-101delT		intron_variant		1	NM_001206641.3	ENSP00000355574.5
COA6	ENST00000366613.1	c.123-101delT		intron_variant		1		ENSP00000355572.1
COA6	ENST00000619305.1	c.-16-101delT		intron_variant		1		ENSP00000479686.1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 84870 AN: 142788 Hom.: 25131 Cov.: 0

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.575

GnomAD4 exome AF: 0.534 AC: 378502 AN: 708710 Hom.: 70628 Cov.: 0 AF XY: 0.532 AC XY: 189879 AN XY: 357092

Gnomad4 AFR exome AF: 0.702

Gnomad4 AMR exome AF: 0.598

Gnomad4 ASJ exome AF: 0.541

Gnomad4 EAS exome AF: 0.490

Gnomad4 SAS exome AF: 0.483

Gnomad4 FIN exome AF: 0.494

Gnomad4 NFE exome AF: 0.535

Gnomad4 OTH exome AF: 0.538

GnomAD4 genome AF: 0.595 AC: 84944 AN: 142878 Hom.: 25165 Cov.: 0 AF XY: 0.590 AC XY: 40978 AN XY: 69410

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.573

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs61077059; hg19: chr1-234509858;