ENST00000513480.2:n.225-22112T>A

Variant names:

• chr5-38766129-A-T
• rs4620043
• ENST00000513480.2:n.225-22112T>A

Variant summary

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

The ENST00000513480.2(OSMR-DT):​n.225-22112T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,128 control chromosomes in the GnomAD database, including 11,583 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 0.39 (11583 hom., cov: 33)
• Consequence: OSMR-DT ENST00000513480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.280-22112T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSMR-DT	ENST00000513480.2	n.225-22112T>A		intron_variant	Intron 2 of 3	4
OSMR-DT	ENST00000636516.3	n.269-22112T>A		intron_variant	Intron 2 of 5	5
OSMR-DT	ENST00000662290.1	n.243+30224T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58662 AN: 152010 Hom.: 11579 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.386 AC: 58685 AN: 152128 Hom.: 11583 Cov.: 33 AF XY: 0.381 AC XY: 28353 AN XY: 74370

African (AFR) AF: 0.452 AC: 18753 AN: 41482

American (AMR) AF: 0.336 AC: 5139 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1346 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1116 AN: 5184

South Asian (SAS) AF: 0.372 AC: 1793 AN: 4814

European-Finnish (FIN) AF: 0.358 AC: 3790 AN: 10576

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25520 AN: 68000

Other (OTH) AF: 0.375 AC: 792 AN: 2114

Alfa AF: 0.384 Hom.: 1425

Bravo AF: 0.385

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.27
DANN	Benign	0.76
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4620043; hg19: chr5-38766231;