17-13830489-C-T

Variant summary

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

The ENST00000582752.7(COX10-DT):n.809+49813G>A 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 0.228 in 152,008 control chromosomes in the GnomAD database, including 4,218 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 0.23 (4218 hom., cov: 32)
• Consequence: COX10-DT ENST00000582752.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506974	XR_001752796.1	n.288-3892G>A		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752794.1	n.288-3892G>A		intron_variant, non_coding_transcript_variant
LOC100506974	XR_001752797.1	n.221-3892G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COX10-DT	ENST00000582752.7	n.809+49813G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34719 AN: 151890 Hom.: 4214 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.228 AC: 34731 AN: 152008 Hom.: 4218 Cov.: 32 AF XY: 0.233 AC XY: 17313 AN XY: 74290

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.223

Alfa AF: 0.234 Hom.: 9831

Bravo AF: 0.233

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.80
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12949531; hg19: chr17-13733806;