rs9894986

chr17-13847624-A-C

Variant summary

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

The ENST00000582752.7(COX10-DT):n.809+32678T>G 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 0.0414 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 ENST00000582752.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

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

LOC100506974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506974	XR_001752796.1	n.288-21027T>G		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752794.1	n.288-21027T>G		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752797.1	n.220+17455T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COX10-DT	ENST00000582752.7	n.809+32678T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.0759

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.0615

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0383 Hom.: 133

Bravo AF: 0.0450

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.44
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9894986; hg19: chr17-13750941;