rs1239345

chr5-38937006-T-C

Variant summary

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

The XM_011514161.3(OSMR):c.2370+4471T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 152,312 control chromosomes in the GnomAD database, including 138 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 0.033 (138 hom., cov: 33)
• Consequence: OSMR XM_011514161.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

OSMR (HGNC:8507): (oncostatin M receptor) This gene encodes a member of the type I cytokine receptor family. The encoded protein heterodimerizes with interleukin 6 signal transducer to form the type II oncostatin M receptor and with interleukin 31 receptor A to form the interleukin 31 receptor, and thus transduces oncostatin M and interleukin 31 induced signaling events. Mutations in this gene have been associated with familial primary localized cutaneous amyloidosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSMR	XM_011514161.3	c.2370+4471T>C		intron_variant
OSMR	XM_017010019.2	c.2367+4471T>C		intron_variant
OSMR	XM_047417872.1	c.2367+4471T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSMR	ENST00000508882.1	c.74+4471T>C		intron_variant, NMD_transcript_variant		3
OSMR	ENST00000509237.5	c.155+4471T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5043 AN: 152194 Hom.: 138 Cov.: 33

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.00827

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.00810

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0331 AC: 5048 AN: 152312 Hom.: 138 Cov.: 33 AF XY: 0.0331 AC XY: 2465 AN XY: 74480

Gnomad4 AFR AF: 0.0640

Gnomad4 AMR AF: 0.0278

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.00868

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.00810

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0212 Hom.: 35

Bravo AF: 0.0336

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1239345; hg19: chr5-38937108;