rs6044284

Variant names:

• chr20-16754044-G-A
• rs6044284
• ENST00000490148.1:n.101+4570G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000490148.1(OTOR):​n.101+4570G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,208 control chromosomes in the GnomAD database, including 923 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 0.10 (923 hom., cov: 32)
• Consequence: OTOR ENST00000490148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 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.101+4570G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15652 AN: 152090 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0645

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.103 AC: 15672 AN: 152208 Hom.: 923 Cov.: 32 AF XY: 0.102 AC XY: 7590 AN XY: 74412

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0941 Hom.: 147

Bravo AF: 0.102

Asia WGS AF: 0.153 AC: 529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.026
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6044284; hg19: chr20-16734689;