rs1029659

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-13984704-C-A
• chr17-13984704-C-T

Variant summary

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

The ENST00000602539.3(COX10-DT):​n.684+49236G>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 ENST00000602539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.261

Alfa AF: 0.231 Hom.: 2282

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1029659; hg19: chr17-13888021;