rs1501742

Variant names:

• chr5-38836602-A-G
• rs1501742
• ENST00000513480.2:n.107+9066T>C

Variant summary

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

The ENST00000513480.2(OSMR-DT):​n.107+9066T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,216 control chromosomes in the GnomAD database, including 2,462 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 0.16 (2462 hom., cov: 32)
• Consequence: OSMR-DT ENST00000513480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513480.2. 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+9066T>C		intron	N/A
	OSMR-DT	NR_171676.1		n.102+9066T>C		intron	N/A
	OSMR-DT	NR_171677.1		n.102+9066T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000513480.2	TSL:4	n.107+9066T>C		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.151+9066T>C		intron	N/A
	OSMR-DT	ENST00000654447.1		n.94+9066T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24619 AN: 152098 Hom.: 2465 Cov.: 32

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.162 AC: 24601 AN: 152216 Hom.: 2462 Cov.: 32 AF XY: 0.165 AC XY: 12264 AN XY: 74442

African (AFR) AF: 0.0575 AC: 2391 AN: 41558

American (AMR) AF: 0.202 AC: 3083 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1131 AN: 5176

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4826

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10598

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13290 AN: 67984

Other (OTH) AF: 0.192 AC: 405 AN: 2114

Alfa AF: 0.191 Hom.: 9150

Bravo AF: 0.157

Asia WGS AF: 0.293 AC: 1017 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.54
PhyloP100		0.26

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: rs1501742;

hg19: chr5-38836704;