rs3763098

chr5-38844887-T-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+781A>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 0.168 in 151,900 control chromosomes in the GnomAD database, including 2,736 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 0.17 (2736 hom., cov: 31)
• Consequence: OSMR-DT NR_109951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSMR-DT	NR_109951.1	n.162+781A>C		intron_variant, non_coding_transcript_variant
OSMR-DT	NR_171676.1	n.102+781A>C		intron_variant, non_coding_transcript_variant
OSMR-DT	NR_171677.1	n.102+781A>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+781A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25543 AN: 151780 Hom.: 2741 Cov.: 31

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.168 AC: 25521 AN: 151900 Hom.: 2736 Cov.: 31 AF XY: 0.170 AC XY: 12596 AN XY: 74238

Gnomad4 AFR AF: 0.0420

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.197

Alfa AF: 0.177 Hom.: 373

Bravo AF: 0.162

Asia WGS AF: 0.231 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763098; hg19: chr5-38844989;