ENST00000490148.1:n.102-4142T>C

Variant names:

• chr20-16760180-T-C
• rs4491792
• ENST00000490148.1:n.102-4142T>C

Variant summary

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

The ENST00000490148.1(OTOR):​n.102-4142T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,334 control chromosomes in the GnomAD database, including 3,382 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 0.21 (3382 hom., cov: 31)
• Consequence: OTOR ENST00000490148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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.102-4142T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31318 AN: 151212 Hom.: 3376 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.207 AC: 31353 AN: 151334 Hom.: 3382 Cov.: 31 AF XY: 0.204 AC XY: 15086 AN XY: 73910

African (AFR) AF: 0.280 AC: 11525 AN: 41216

American (AMR) AF: 0.239 AC: 3633 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1270 AN: 5118

South Asian (SAS) AF: 0.0792 AC: 380 AN: 4796

European-Finnish (FIN) AF: 0.150 AC: 1555 AN: 10400

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11762 AN: 67836

Other (OTH) AF: 0.204 AC: 428 AN: 2102

Alfa AF: 0.185 Hom.: 4439

Bravo AF: 0.219

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4491792; hg19: chr20-16740825;