rs540558

Variant names:

• chr5-38844171-C-G
• rs540558
• ENST00000512519.2:n.166-234G>C

Variant summary

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

The ENST00000512519.2(OSMR-DT):​n.166-234G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,022 control chromosomes in the GnomAD database, including 2,638 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 0.18 (2638 hom., cov: 32)
• Consequence: OSMR-DT ENST00000512519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512519.2. 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.162+1497G>C		intron	N/A
	OSMR-DT	NR_171676.1		n.102+1497G>C		intron	N/A
	OSMR-DT	NR_171677.1		n.102+1497G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000512519.2	TSL:2	n.166-234G>C		intron	N/A
	OSMR-DT	ENST00000513480.2	TSL:4	n.107+1497G>C		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.151+1497G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27942 AN: 151904 Hom.: 2636 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.184 AC: 27955 AN: 152022 Hom.: 2638 Cov.: 32 AF XY: 0.186 AC XY: 13818 AN XY: 74300

African (AFR) AF: 0.196 AC: 8121 AN: 41468

American (AMR) AF: 0.190 AC: 2909 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3466

East Asian (EAS) AF: 0.0592 AC: 306 AN: 5168

South Asian (SAS) AF: 0.191 AC: 921 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2446 AN: 10536

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12072 AN: 67966

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.178 Hom.: 301

Bravo AF: 0.179

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs540558; hg19: chr5-38844273;