Genetic Variant OSMR-DT:n.165+364delT (chr5-38845303-CA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000512519.2(OSMR-DT):n.165+364delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.029 ( 180 hom., cov: 0)

Consequence

OSMR-DT
ENST00000512519.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

1 publications found

Variant links:

Genes affected

OSMR-DT (HGNC:50296): (OSMR divergent transcript)

OSMR-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
OSMR-DT	NR_109951.1 link	n.162+364delT	intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1 link	n.102+364delT	intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1 link	n.102+364delT	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OSMR-DT	ENST00000512519.2 link	n.165+364delT	intron_variant	Intron 1 of 1	2
OSMR-DT	ENST00000513480.2 link	n.107+364delT	intron_variant	Intron 1 of 3	4
OSMR-DT	ENST00000636516.3 link	n.151+364delT	intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.0293

AC:

2627

AN:

89640

Hom.:

181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00666

Gnomad AMI

AF:

0.00885

Gnomad AMR

AF:

0.0203

Gnomad ASJ

AF:

0.0122

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.0357

Gnomad FIN

AF:

0.0107

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0169

Gnomad OTH

AF:

0.0458

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

GnomAD4 genome

AF:

0.0292

AC:

2616

AN:

89620

Hom.:

180

Cov.:

AF XY:

0.0313

AC XY:

1287

AN XY:

41142

show subpopulations

African (AFR)

AF:

0.00665

AC:

146

AN:

21958

American (AMR)

AF:

0.0203

AC:

153

AN:

7544

Ashkenazi Jewish (ASJ)

AF:

0.0122

AC:

AN:

2542

East Asian (EAS)

AF:

0.377

AC:

1318

AN:

3496

South Asian (SAS)

AF:

0.0348

AC:

AN:

2412

European-Finnish (FIN)

AF:

0.0107

AC:

AN:

2702

Middle Eastern (MID)

AF:

0.00

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.0169

AC:

794

AN:

46966

Other (OTH)

AF:

0.0472

AC:

AN:

1166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.448

Heterozygous variant carriers

161

241

322

402

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.4

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over