17-13984704-C-A

Variant names:

• chr17-13984704-C-A
• rs1029659
• ENST00000582752.7:n.621+49304G>T

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+49304G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 140,470 control chromosomes in the GnomAD database, including 5,476 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 0.27 (5476 hom., cov: 25)
• Consequence: COX10-DT ENST00000582752.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COX10-DT	ENST00000582752.7	n.621+49304G>T		intron_variant	Intron 2 of 4	3
COX10-DT	ENST00000602539.3	n.684+49236G>T		intron_variant	Intron 2 of 4	2
COX10-DT	ENST00000602743.1	n.224+84568G>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.270 AC: 37929 AN: 140394 Hom.: 5480 Cov.: 25

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.270 AC: 37947 AN: 140470 Hom.: 5476 Cov.: 25 AF XY: 0.280 AC XY: 18899 AN XY: 67428

African (AFR) AF: 0.318 AC: 11884 AN: 37426

American (AMR) AF: 0.374 AC: 5184 AN: 13846

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 657 AN: 3388

East Asian (EAS) AF: 0.499 AC: 2389 AN: 4786

South Asian (SAS) AF: 0.293 AC: 1279 AN: 4368

European-Finnish (FIN) AF: 0.339 AC: 2658 AN: 7830

Middle Eastern (MID) AF: 0.173 AC: 47 AN: 272

European-Non Finnish (NFE) AF: 0.202 AC: 13273 AN: 65726

Other (OTH) AF: 0.261 AC: 504 AN: 1930

Alfa AF: 0.230 Hom.: 2473

Bravo AF: 0.274

Asia WGS AF: 0.408 AC: 1416 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1029659; hg19: chr17-13888021;