rs1428499

chr5-38694381-G-T

Variant summary

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

The NR_109951.1(OSMR-DT):n.371-882C>A 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 0.19 in 152,166 control chromosomes in the GnomAD database, including 3,290 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 0.19 (3290 hom., cov: 32)
• Consequence: OSMR-DT NR_109951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

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 (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSMR-DT	NR_109951.1	n.371-882C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSMR-DT	ENST00000662290.1	n.244-1014C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28959 AN: 152046 Hom.: 3291 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.190 AC: 28956 AN: 152166 Hom.: 3290 Cov.: 32 AF XY: 0.193 AC XY: 14354 AN XY: 74356

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.0958

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.202

Alfa AF: 0.234 Hom.: 3144

Bravo AF: 0.174

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1428499; hg19: chr5-38694483;