rs540558

Positions:

• chr5-38844171-C-G

Variant summary

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

The ENST00000512519.1(OSMR-DT):​n.163-234G>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 ENST00000512519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

OSMR-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.162+1497G>C		intron_variant
OSMR-DT	NR_171676.1	n.102+1497G>C		intron_variant
OSMR-DT	NR_171677.1	n.102+1497G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSMR-DT	ENST00000512519.1	n.163-234G>C		intron_variant		2
OSMR-DT	ENST00000513480.1	n.101+1497G>C		intron_variant		4
OSMR-DT	ENST00000636516.2	n.126+1497G>C		intron_variant		5

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0592

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.173

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs540558; hg19: chr5-38844273;