rs9292715

Variant names:

• chr5-38681565-T-C
• rs9292715
• ENST00000847647.1:n.415+4407A>G

Variant summary

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

The ENST00000847647.1(OSMR-DT):​n.415+4407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,304 control chromosomes in the GnomAD database, including 643 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 0.058 (643 hom., cov: 33)
• Consequence: OSMR-DT ENST00000847647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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
OSMR-DT	ENST00000847647.1	n.415+4407A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8754 AN: 152186 Hom.: 633 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00611

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0578 AC: 8797 AN: 152304 Hom.: 643 Cov.: 33 AF XY: 0.0558 AC XY: 4156 AN XY: 74474

African (AFR) AF: 0.172 AC: 7133 AN: 41538

American (AMR) AF: 0.0568 AC: 869 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0173 AC: 90 AN: 5192

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4826

European-Finnish (FIN) AF: 0.00988 AC: 105 AN: 10628

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00610 AC: 415 AN: 68038

Other (OTH) AF: 0.0468 AC: 99 AN: 2116

Alfa AF: 0.0377 Hom.: 60

Bravo AF: 0.0671

Asia WGS AF: 0.0550 AC: 189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.60
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs9292715; hg19: chr5-38681667;