17-13781600-C-A

Variant names:

• chr17-13781600-C-A
• rs4792394
• ENST00000423323.2:n.2283-4251G>T

Variant summary

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

The ENST00000423323.2(COX10-DT):​n.2283-4251G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,758 control chromosomes in the GnomAD database, including 21,938 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 0.53 (21938 hom., cov: 32)
• Consequence: COX10-DT ENST00000423323.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 11 publications found

Genes affected

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

LOC107985014 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423323.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX10-DT	ENST00000423323.2	TSL:2	n.2283-4251G>T		intron	N/A
	COX10-DT	ENST00000577798.6	TSL:3	n.419-4251G>T		intron	N/A
	COX10-DT	ENST00000582752.7	TSL:3	n.810-24871G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81108 AN: 151640 Hom.: 21927 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.535 AC: 81161 AN: 151758 Hom.: 21938 Cov.: 32 AF XY: 0.536 AC XY: 39802 AN XY: 74190

African (AFR) AF: 0.542 AC: 22390 AN: 41338

American (AMR) AF: 0.476 AC: 7257 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1786 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3626 AN: 5156

South Asian (SAS) AF: 0.530 AC: 2552 AN: 4818

European-Finnish (FIN) AF: 0.575 AC: 6045 AN: 10504

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35834 AN: 67922

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

Alfa AF: 0.528 Hom.: 73868

Bravo AF: 0.526

Asia WGS AF: 0.597 AC: 2068 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.3
DANN	Benign	0.82
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs4792394; hg19: chr17-13684917;