17-13787437-A-G

Position:

• chr17-13787437-A-G

Variant summary

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

The ENST00000582752.7(COX10-DT):​n.810-30708T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,964 control chromosomes in the GnomAD database, including 14,901 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 0.43 (14901 hom., cov: 31)
• Consequence: COX10-DT ENST00000582752.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

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

LOC107985014 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985014	XR_007065628.1	n.43+2832T>C		intron_variant, non_coding_transcript_variant
LOC107985014	XR_007065626.1	n.43+2832T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COX10-DT	ENST00000582752.7	n.810-30708T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65400 AN: 151846 Hom.: 14887 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.431 AC: 65441 AN: 151964 Hom.: 14901 Cov.: 31 AF XY: 0.429 AC XY: 31901 AN XY: 74292

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.436

Alfa AF: 0.479 Hom.: 22745

Bravo AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2322969; hg19: chr17-13690754;