rs7215286

Variant names:

• chr17-13805544-C-G
• rs7215286
• ENST00000577798.6:n.374-15231G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-13805544-C-G
• chr17-13805544-C-T

Variant summary

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

The ENST00000602539.3(COX10-DT):​n.870-28195G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 152,016 control chromosomes in the GnomAD database, including 1,136 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 0.095 (1136 hom., cov: 29)
• Consequence: COX10-DT ENST00000602539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.632
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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.374-15231G>C		intron	N/A
	COX10-DT	ENST00000582752.7	TSL:3	n.810-48815G>C		intron	N/A
	COX10-DT	ENST00000602539.3	TSL:2	n.870-28195G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0955 AC: 14501 AN: 151898 Hom.: 1131 Cov.: 29

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0124

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0955 AC: 14517 AN: 152016 Hom.: 1136 Cov.: 29 AF XY: 0.0930 AC XY: 6908 AN XY: 74310

African (AFR) AF: 0.217 AC: 8966 AN: 41396

American (AMR) AF: 0.0565 AC: 863 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.0329 AC: 170 AN: 5166

South Asian (SAS) AF: 0.0728 AC: 351 AN: 4820

European-Finnish (FIN) AF: 0.0124 AC: 131 AN: 10588

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0490 AC: 3333 AN: 67984

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.0462 Hom.: 137

Bravo AF: 0.103

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.77
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism

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: rs7215286;

hg19: chr17-13708861;