rs9894986

Variant names:

• chr17-13847624-A-C
• rs9894986
• ENST00000577798.6:n.373+17455T>G

Variant summary

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

The ENST00000602539.3(COX10-DT):​n.869+32678T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,164 control chromosomes in the GnomAD database, including 145 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 0.041 (145 hom., cov: 32)
• Consequence: COX10-DT ENST00000602539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

Genes affected

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

LOC100506974 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.0723 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	ENST00000577798.6	TSL:3	n.373+17455T>G		intron	N/A
	COX10-DT	ENST00000582752.7	TSL:3	n.809+32678T>G		intron	N/A
	COX10-DT	ENST00000602539.3	TSL:2	n.869+32678T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6291 AN: 152046 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.0485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0414 AC: 6299 AN: 152164 Hom.: 145 Cov.: 32 AF XY: 0.0422 AC XY: 3142 AN XY: 74386

African (AFR) AF: 0.0484 AC: 2011 AN: 41560

American (AMR) AF: 0.0759 AC: 1159 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3470

East Asian (EAS) AF: 0.0615 AC: 319 AN: 5184

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4826

European-Finnish (FIN) AF: 0.0105 AC: 111 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0335 AC: 2278 AN: 67920

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0392 Hom.: 167

Bravo AF: 0.0450

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.85
PhyloP100		-1.0

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: rs9894986;

hg19: chr17-13750941;