chr17-13805544-C-G

Position:

• chr17-13805544-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.810-48815G>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 0.0955 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 ENST00000582752.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.632

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506974	XR_001752796.1	n.388-14511G>C		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752794.1	n.388-14469G>C		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752797.1	n.321-14469G>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.810-48815G>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0565

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.0124

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.0957

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7215286; hg19: chr17-13708861;