rs4491792

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-16760180-T-C
• chr20-16760180-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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.102-4142T>C		intron_variant	Intron 1 of 2	4

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.204

Alfa AF: 0.181 Hom.: 2651

Bravo AF: 0.219

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4491792; hg19: chr20-16740825;