Genetic Variant OSMR-DT:n.165+364_165+365insTTT (chr5-38845303-C-CAAA) – 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+365insTTT 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 0.032 ( 206 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 (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
OSMR-DT	NR_109951.1 link	n.162+362_162+364dupTTT	intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1 link	n.102+362_102+364dupTTT	intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1 link	n.102+362_102+364dupTTT	intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0322

AC:

2883

AN:

89522

Hom.:

207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.00147

Gnomad AMR

AF:

0.0141

Gnomad ASJ

AF:

0.00236

Gnomad EAS

AF:

0.00141

Gnomad SAS

AF:

0.00615

Gnomad FIN

AF:

0.00185

Gnomad MID

AF:

0.0301

Gnomad NFE

AF:

0.00335

Gnomad OTH

AF:

0.0181

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

GnomAD4 genome

AF:

0.0322

AC:

2884

AN:

89502

Hom.:

206

Cov.:

AF XY:

0.0329

AC XY:

1353

AN XY:

41100

show subpopulations

African (AFR)

AF:

0.117

AC:

2564

AN:

21900

American (AMR)

AF:

0.0141

AC:

106

AN:

7528

Ashkenazi Jewish (ASJ)

AF:

0.00236

AC:

AN:

2538

East Asian (EAS)

AF:

0.00142

AC:

AN:

3518

South Asian (SAS)

AF:

0.00621

AC:

AN:

2414

European-Finnish (FIN)

AF:

0.00185

AC:

AN:

2704

Middle Eastern (MID)

AF:

0.0256

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.00335

AC:

157

AN:

46898

Other (OTH)

AF:

0.0180

AC:

AN:

1168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

120

239

359

478

598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<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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5-38845303-CAAAAAAAA-CAAAAAAAAAAA

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