rs6080400

Variant names:

• chr20-16763266-C-T
• rs6080400
• ENST00000490148.1:n.102-1056C>T

Variant summary

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

The ENST00000490148.1(OTOR):​n.102-1056C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,954 control chromosomes in the GnomAD database, including 8,465 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 0.32 (8465 hom., cov: 32)
• Consequence: OTOR ENST00000490148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 3 publications found

Genes affected

OTOR (HGNC:8517): (otoraplin) This gene encodes a member of the melanoma-inhibiting activity gene family. The encoded protein is secreted via the Golgi apparatus and may function in cartilage development and maintenance. A frequent polymorphism in the translation start codon of this gene can abolish translation and may be associated with forms of deafness. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490148.1. 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
	OTOR	ENST00000490148.1	TSL:4	n.102-1056C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49133 AN: 151836 Hom.: 8455 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.324 AC: 49165 AN: 151954 Hom.: 8465 Cov.: 32 AF XY: 0.321 AC XY: 23869 AN XY: 74250

African (AFR) AF: 0.235 AC: 9732 AN: 41470

American (AMR) AF: 0.264 AC: 4031 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3468

East Asian (EAS) AF: 0.127 AC: 656 AN: 5168

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4810

European-Finnish (FIN) AF: 0.456 AC: 4798 AN: 10516

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26572 AN: 67956

Other (OTH) AF: 0.300 AC: 631 AN: 2100

Alfa AF: 0.363 Hom.: 43503

Bravo AF: 0.305

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.81
PhyloP100		-0.13

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: rs6080400;

hg19: chr20-16743911;