5-38818179-T-C

Variant names:

• chr5-38818179-T-C
• rs386994
• ENST00000513480.1:n.102-21710A>G

Variant summary

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

The ENST00000513480.1(OSMR-DT):​n.102-21710A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,062 control chromosomes in the GnomAD database, including 50,052 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 0.81 (50052 hom., cov: 31)
• Consequence: OSMR-DT ENST00000513480.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.163-21710A>G		intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1	n.103-4468A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSMR-DT	ENST00000513480.1	n.102-21710A>G		intron_variant	Intron 1 of 3	4
OSMR-DT	ENST00000636516.2	n.127-21710A>G		intron_variant	Intron 1 of 5	5
OSMR-DT	ENST00000662290.1	n.127-21710A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123188 AN: 151944 Hom.: 50008 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.811 AC: 123289 AN: 152062 Hom.: 50052 Cov.: 31 AF XY: 0.810 AC XY: 60230 AN XY: 74350

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.822

Alfa AF: 0.815 Hom.: 62198

Bravo AF: 0.815

Asia WGS AF: 0.879 AC: 3051 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386994; hg19: chr5-38818281;