ENST00000582752.7:n.621+26776G>A

Variant names:

• chr17-14007232-C-T
• rs17608059
• ENST00000582752.7:n.621+26776G>A

Variant summary

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

The ENST00000582752.7(COX10-DT):​n.621+26776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,684 control chromosomes in the GnomAD database, including 13,732 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 0.42 (13732 hom., cov: 29)
• Consequence: COX10-DT ENST00000582752.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 14 publications found

Genes affected

COX10-DT (HGNC:38873): (COX10 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582752.7. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX10-DT	ENST00000582752.7	TSL:3	n.621+26776G>A		intron	N/A
	COX10-DT	ENST00000602539.3	TSL:2	n.684+26708G>A		intron	N/A
	COX10-DT	ENST00000602743.1	TSL:5	n.224+62040G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63078 AN: 151566 Hom.: 13718 Cov.: 29

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.416 AC: 63120 AN: 151684 Hom.: 13732 Cov.: 29 AF XY: 0.419 AC XY: 31023 AN XY: 74108

African (AFR) AF: 0.295 AC: 12209 AN: 41354

American (AMR) AF: 0.352 AC: 5370 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1723 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2395 AN: 5124

South Asian (SAS) AF: 0.466 AC: 2240 AN: 4802

European-Finnish (FIN) AF: 0.513 AC: 5388 AN: 10504

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32145 AN: 67862

Other (OTH) AF: 0.453 AC: 958 AN: 2116

Alfa AF: 0.448 Hom.: 48973

Bravo AF: 0.401

Asia WGS AF: 0.476 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.46
PhyloP100		-0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17608059; hg19: chr17-13910549;