rs1428499

Variant names:

• chr5-38694381-G-T
• rs1428499
• ENST00000662290.1:n.244-1014C>A

Variant summary

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

The ENST00000662290.1(OSMR-DT):​n.244-1014C>A variant causes a intron 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 ENST00000662290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 2 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=-0.87).
• 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 rank	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.371-882C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSMR-DT	ENST00000662290.1	n.244-1014C>A		intron_variant	Intron 2 of 4
OSMR-DT	ENST00000847593.1	n.290-8258C>A		intron_variant	Intron 3 of 3
OSMR-DT	ENST00000847594.1	n.258-1014C>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0754 AC: 3133 AN: 41536

American (AMR) AF: 0.172 AC: 2627 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3472

East Asian (EAS) AF: 0.0958 AC: 496 AN: 5180

South Asian (SAS) AF: 0.240 AC: 1154 AN: 4816

European-Finnish (FIN) AF: 0.291 AC: 3070 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16912 AN: 67990

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.222 Hom.: 9854

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1428499; hg19: chr5-38694483;