Genetic Variant ENST00000512519.2:n.165+364_165+365insTT (chr5-38845303-C-CAA) – 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+364_165+365insTT 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 0.19 ( 1854 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 (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
OSMR-DT	NR_109951.1 link	n.162+363_162+364dupTT	intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1 link	n.102+363_102+364dupTT	intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1 link	n.102+363_102+364dupTT	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OSMR-DT	ENST00000512519.2 link	n.165+364_165+365insTT	intron_variant	Intron 1 of 1	2
OSMR-DT	ENST00000513480.2 link	n.107+364_107+365insTT	intron_variant	Intron 1 of 3	4
OSMR-DT	ENST00000636516.3 link	n.151+364_151+365insTT	intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

17076

AN:

89280

Hom.:

1853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.0728

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.167

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.191

AC:

17077

AN:

89262

Hom.:

1854

Cov.:

AF XY:

0.190

AC XY:

7771

AN XY:

40982

show subpopulations

African (AFR)

AF:

0.192

AC:

4189

AN:

21874

American (AMR)

AF:

0.189

AC:

1426

AN:

7526

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

493

AN:

2526

East Asian (EAS)

AF:

0.0734

AC:

258

AN:

3516

South Asian (SAS)

AF:

0.178

AC:

429

AN:

2404

European-Finnish (FIN)

AF:

0.189

AC:

507

AN:

2688

Middle Eastern (MID)

AF:

0.178

AC:

AN:

152

European-Non Finnish (NFE)

AF:

0.201

AC:

9407

AN:

46738

Other (OTH)

AF:

0.183

AC:

213

AN:

1162

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

624

1247

1871

2494

3118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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

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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