17-13968125-T-G

Variant names:

• chr17-13968125-T-G
• rs8069913
• ENST00000582752.7:n.621+65883A>C

Variant summary

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

The ENST00000602539.3(COX10-DT):​n.684+65815A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,168 control chromosomes in the GnomAD database, including 2,372 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 0.15 (2372 hom., cov: 32)
• Consequence: COX10-DT ENST00000602539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602539.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX10-DT	ENST00000582752.7	TSL:3	n.621+65883A>C		intron	N/A
	COX10-DT	ENST00000602539.3	TSL:2	n.684+65815A>C		intron	N/A
	COX10-DT	ENST00000602743.1	TSL:5	n.225-69393A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23156 AN: 152050 Hom.: 2372 Cov.: 32

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.152 AC: 23156 AN: 152168 Hom.: 2372 Cov.: 32 AF XY: 0.149 AC XY: 11054 AN XY: 74382

African (AFR) AF: 0.0400 AC: 1661 AN: 41534

American (AMR) AF: 0.120 AC: 1840 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 661 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5166

South Asian (SAS) AF: 0.0838 AC: 404 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2283 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15669 AN: 67988

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.188 Hom.: 1608

Bravo AF: 0.143

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8069913;

hg19: chr17-13871442;