17-14007232-C-T

Variant names:

• chr17-14007232-C-T
• rs17608059
• ENST00000582752.7:n.621+26776G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602539.3(COX10-DT):​n.684+26708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,684 control chromosomes in the GnomAD database, including 13,732 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 0.42 (13732 hom., cov: 29)
• Consequence: COX10-DT ENST00000602539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COX10-DT	ENST00000582752.7	n.621+26776G>A		intron_variant	Intron 2 of 4	3
COX10-DT	ENST00000602539.3	n.684+26708G>A		intron_variant	Intron 2 of 4	2
COX10-DT	ENST00000602743.1	n.224+62040G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63078 AN: 151566 Hom.: 13718 Cov.: 29

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.416 AC: 63120 AN: 151684 Hom.: 13732 Cov.: 29 AF XY: 0.419 AC XY: 31023 AN XY: 74108

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.453

Alfa AF: 0.459 Hom.: 33222

Bravo AF: 0.401

Asia WGS AF: 0.476 AC: 1659 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	0.21
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17608059; hg19: chr17-13910549;