rs7208809

chr17-13834006-C-Achr17-13834006-C-G

Variant summary

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

The ENST00000582752.7(COX10-DT):n.809+46296G>T 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 0.0871 in 152,222 control chromosomes in the GnomAD database, including 622 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 0.087 (622 hom., cov: 33)
• Consequence: COX10-DT ENST00000582752.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506974	XR_001752796.1	n.288-7409G>T		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752794.1	n.288-7409G>T		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752797.1	n.221-7409G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COX10-DT	ENST00000582752.7	n.809+46296G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13234 AN: 152104 Hom.: 620 Cov.: 33

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.0871 AC: 13252 AN: 152222 Hom.: 622 Cov.: 33 AF XY: 0.0899 AC XY: 6693 AN XY: 74424

Gnomad4 AFR AF: 0.0595

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0815

Gnomad4 EAS AF: 0.0646

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.0519 Hom.: 54

Bravo AF: 0.0826

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.3
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7208809; hg19: chr17-13737323;