rs3763098

Variant names:

• chr5-38844887-T-G
• rs3763098
• ENST00000512519.2:n.165+781A>C

Variant summary

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

The ENST00000512519.2(OSMR-DT):​n.165+781A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,900 control chromosomes in the GnomAD database, including 2,736 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 0.17 (2736 hom., cov: 31)
• Consequence: OSMR-DT ENST00000512519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 1 publications found

Genes affected

OSMR-DT (HGNC:50296): (OSMR divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512519.2. 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
	OSMR-DT	NR_109951.1		n.162+781A>C		intron	N/A
	OSMR-DT	NR_171676.1		n.102+781A>C		intron	N/A
	OSMR-DT	NR_171677.1		n.102+781A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000512519.2	TSL:2	n.165+781A>C		intron	N/A
	OSMR-DT	ENST00000513480.2	TSL:4	n.107+781A>C		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.151+781A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25543 AN: 151780 Hom.: 2741 Cov.: 31

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.168 AC: 25521 AN: 151900 Hom.: 2736 Cov.: 31 AF XY: 0.170 AC XY: 12596 AN XY: 74238

African (AFR) AF: 0.0420 AC: 1741 AN: 41428

American (AMR) AF: 0.211 AC: 3216 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3468

East Asian (EAS) AF: 0.149 AC: 764 AN: 5128

South Asian (SAS) AF: 0.330 AC: 1588 AN: 4806

European-Finnish (FIN) AF: 0.174 AC: 1830 AN: 10536

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14832 AN: 67940

Other (OTH) AF: 0.197 AC: 417 AN: 2116

Alfa AF: 0.177 Hom.: 373

Bravo AF: 0.162

Asia WGS AF: 0.231 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-1.8

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: rs3763098;

hg19: chr5-38844989;