rs1501742

chr5-38836602-A-G

Variant summary

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

The NR_109951.1(OSMR-DT):n.162+9066T>C variant causes a intron, non coding transcript 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 NR_109951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSMR-DT	NR_109951.1	n.162+9066T>C		intron_variant, non_coding_transcript_variant
OSMR-DT	NR_171676.1	n.102+9066T>C		intron_variant, non_coding_transcript_variant
OSMR-DT	NR_171677.1	n.102+9066T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSMR-DT	ENST00000662290.1	n.126+9066T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0575

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.192

Alfa AF: 0.201 Hom.: 6259

Bravo AF: 0.157

Asia WGS AF: 0.293 AC: 1017 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.5
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1501742; hg19: chr5-38836704;