rs4411532

chr17-13949656-G-A

Variant summary

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

The ENST00000582752.7(COX10-DT):n.622-56814C>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 0.552 in 152,014 control chromosomes in the GnomAD database, including 26,315 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 0.55 (26315 hom., cov: 32)
• Consequence: COX10-DT ENST00000582752.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COX10-DT	ENST00000582752.7	n.622-56814C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83839 AN: 151902 Hom.: 26318 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.552 AC: 83855 AN: 152014 Hom.: 26315 Cov.: 32 AF XY: 0.546 AC XY: 40526 AN XY: 74284

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.587

Alfa AF: 0.598 Hom.: 8167

Bravo AF: 0.532

Asia WGS AF: 0.506 AC: 1761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.91
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4411532; hg19: chr17-13852973;