rs7208809

Variant names:

• chr17-13834006-C-A
• rs7208809
• ENST00000577798.6:n.373+31073G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-13834006-C-A
• chr17-13834006-C-G

Variant summary

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

The ENST00000602539.3(COX10-DT):​n.869+46296G>T variant causes a intron 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 ENST00000602539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 2 publications found

Genes affected

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

LOC100506974 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602539.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX10-DT	ENST00000577798.6	TSL:3	n.373+31073G>T		intron	N/A
	COX10-DT	ENST00000582752.7	TSL:3	n.809+46296G>T		intron	N/A
	COX10-DT	ENST00000602539.3	TSL:2	n.869+46296G>T		intron	N/A

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

African (AFR) AF: 0.0595 AC: 2469 AN: 41530

American (AMR) AF: 0.102 AC: 1561 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 283 AN: 3472

East Asian (EAS) AF: 0.0646 AC: 334 AN: 5174

South Asian (SAS) AF: 0.119 AC: 575 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1198 AN: 10590

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0957 AC: 6514 AN: 68032

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.0524 Hom.: 57

Bravo AF: 0.0826

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.56
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7208809;

hg19: chr17-13737323;