rs1029659

Positions:

• 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 ENST00000582752.7(COX10-DT):​n.621+49304G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COX10-DT	ENST00000582752.7	n.621+49304G>T		intron_variant, non_coding_transcript_variant		3

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;