rs6111277

Variant names:

• chr20-16767093-G-A
• rs6111277
• ENST00000490148.1:n.183-2581G>A

Variant summary

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

The ENST00000490148.1(OTOR):​n.183-2581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,098 control chromosomes in the GnomAD database, including 6,781 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 0.28 (6781 hom., cov: 32)
• Consequence: OTOR ENST00000490148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• 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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 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.183-2581G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43123 AN: 151980 Hom.: 6773 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.284 AC: 43147 AN: 152098 Hom.: 6781 Cov.: 32 AF XY: 0.285 AC XY: 21171 AN XY: 74330

African (AFR) AF: 0.159 AC: 6582 AN: 41500

American (AMR) AF: 0.287 AC: 4385 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3470

East Asian (EAS) AF: 0.127 AC: 656 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1235 AN: 4824

European-Finnish (FIN) AF: 0.419 AC: 4428 AN: 10564

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24020 AN: 67966

Other (OTH) AF: 0.272 AC: 573 AN: 2108

Alfa AF: 0.314 Hom.: 3643

Bravo AF: 0.269

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	10
DANN	Benign	0.51
PhyloP100		1.1

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: rs6111277;

hg19: chr20-16747738;