Genetic Variant ENST00000512519.2:n.165+364_165+365insTTTT (chr5-38845303-C-CAAAA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000512519.2(OSMR-DT):n.165+364_165+365insTTTT 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 0.00028 ( 2 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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
OSMR-DT	NR_109951.1 link	n.162+361_162+364dupTTTT	intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1 link	n.102+361_102+364dupTTTT	intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1 link	n.102+361_102+364dupTTTT	intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.000279

AC:

AN:

89628

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000958

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000283

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000639

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.000279

AC:

AN:

89608

Hom.:

Cov.:

AF XY:

0.000243

AC XY:

AN XY:

41128

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000958

AC:

AN:

21932

American (AMR)

AF:

0.00

AC:

AN:

7538

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2540

East Asian (EAS)

AF:

0.000284

AC:

AN:

3518

South Asian (SAS)

AF:

0.00

AC:

AN:

2408

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2702

Middle Eastern (MID)

AF:

0.00

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.0000639

AC:

AN:

46968

Other (OTH)

AF:

0.00

AC:

AN:

1168

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000006), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.375

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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