1-234378125-C-A

Position:

• chr1-234378125-C-A

Variant summary

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

The NM_001206641.3(COA6):​c.372+3736C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,964 control chromosomes in the GnomAD database, including 24,356 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 0.55 (24356 hom., cov: 32)
• Consequence: COA6 NM_001206641.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COA6	NM_001206641.3	c.372+3736C>A		intron_variant		ENST00000366615.10
COA6	NM_001012985.2	c.282+3736C>A		intron_variant
COA6	NM_001301733.1	c.144+3736C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COA6	ENST00000366615.10	c.372+3736C>A		intron_variant		1	NM_001206641.3
COA6	ENST00000366612.1	c.144+3736C>A		intron_variant		1		P1
COA6	ENST00000366613.1	c.282+3736C>A		intron_variant		1
COA6	ENST00000619305.1	c.144+3736C>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82912 AN: 151844 Hom.: 24308 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.546 AC: 83008 AN: 151964 Hom.: 24356 Cov.: 32 AF XY: 0.540 AC XY: 40091 AN XY: 74266

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.531

Alfa AF: 0.469 Hom.: 28054

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.56

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: rs2752; hg19: chr1-234513871;