rs10521250

Positions:

• chr17-14039686-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000449363.2(COX10-DT):​n.208-5270A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 152,318 control chromosomes in the GnomAD database, including 39 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 0.017 (39 hom., cov: 32)
• Consequence: COX10-DT ENST00000449363.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905

Genes affected

COX10-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0175 (2663/152318) while in subpopulation NFE AF= 0.0258 (1754/68026). AF 95% confidence interval is 0.0248. There are 39 homozygotes in gnomad4. There are 1319 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 39 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COX10-DT	NR_049718.1	n.188-5270A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COX10-DT	ENST00000449363.2	n.208-5270A>G		intron_variant		2
COX10-DT	ENST00000582752.7	n.213-5270A>G		intron_variant		3
COX10-DT	ENST00000602539.3	n.208-5270A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0175 AC: 2661 AN: 152200 Hom.: 38 Cov.: 32

Gnomad AFR AF: 0.00444

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0258

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0175 AC: 2663 AN: 152318 Hom.: 39 Cov.: 32 AF XY: 0.0177 AC XY: 1319 AN XY: 74474

Gnomad4 AFR AF: 0.00442

Gnomad4 AMR AF: 0.0100

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0258

Gnomad4 OTH AF: 0.0184

Alfa AF: 0.0239 Hom.: 4

Bravo AF: 0.0152

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521250; hg19: chr17-13943003;