5-38818179-T-C

Variant names:

• chr5-38818179-T-C
• rs386994
• ENST00000847635.1:n.155A>G

Variant summary

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

The ENST00000847635.1(OSMR-DT):​n.155A>G variant causes a non coding transcript exon 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 ENST00000847635.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847635.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	NR_109951.1		n.163-21710A>G		intron	N/A
	OSMR-DT	NR_171676.1		n.103-4468A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000847635.1		n.155A>G		non_coding_transcript_exon	Exon 2 of 4
	OSMR-DT	ENST00000513480.2	TSL:4	n.108-21710A>G		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.152-21710A>G		intron	N/A

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

African (AFR) AF: 0.797 AC: 33044 AN: 41442

American (AMR) AF: 0.805 AC: 12306 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2899 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4861 AN: 5168

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4822

European-Finnish (FIN) AF: 0.768 AC: 8096 AN: 10548

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55378 AN: 68004

Other (OTH) AF: 0.822 AC: 1737 AN: 2114

Alfa AF: 0.815 Hom.: 73730

Bravo AF: 0.815

Asia WGS AF: 0.879 AC: 3051 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.43
PhyloP100		-0.097

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs386994;

hg19: chr5-38818281;