rs451298

Variant names:

• chr5-38830233-A-C
• rs451298
• ENST00000513480.2:n.107+15435T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-38830233-A-C
• chr5-38830233-A-G
• chr5-38830233-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000513480.2(OSMR-DT):​n.107+15435T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: OSMR-DT ENST00000513480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	NR_109951.1		n.162+15435T>G		intron	N/A
	OSMR-DT	NR_171676.1		n.102+15435T>G		intron	N/A
	OSMR-DT	NR_171677.1		n.103-7523T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000513480.2	TSL:4	n.107+15435T>G		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.151+15435T>G		intron	N/A
	OSMR-DT	ENST00000654447.1		n.95-7523T>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs451298; hg19: chr5-38830335;