chr20-16763266-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTOR	ENST00000490148.1	n.102-1056C>T		intron_variant	Intron 1 of 2	4

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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.300

Alfa AF: 0.366 Hom.: 21256

Bravo AF: 0.305

Asia WGS AF: 0.219 AC: 762 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	1.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6080400; hg19: chr20-16743911;