dbSNP rs5867434: OSMR-DT:n.165+357_165+364delTTTTTTTT (chr5-38845303-CAAAAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000512519.2(OSMR-DT):n.165+357_165+364delTTTTTTTT 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 0.000011 ( 0 hom., cov: 0)

Consequence

OSMR-DT
ENST00000512519.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228

Publications

1 publications found

Variant links:

Genes affected

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

OSMR-DT links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000512519.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512519.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
OSMR-DT	NR_109951.1	n.162+357_162+364delTTTTTTTT	intron	N/A
OSMR-DT	NR_171676.1	n.102+357_102+364delTTTTTTTT	intron	N/A
OSMR-DT	NR_171677.1	n.102+357_102+364delTTTTTTTT	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
OSMR-DT	ENST00000512519.2	TSL:2	n.165+357_165+364delTTTTTTTT	intron	N/A
OSMR-DT	ENST00000513480.2	TSL:4	n.107+357_107+364delTTTTTTTT	intron	N/A
OSMR-DT	ENST00000636516.3	TSL:5	n.151+357_151+364delTTTTTTTT	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000111

AC:

AN:

89698

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000456

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.0000112

AC:

AN:

89678

Hom.:

Cov.:

AF XY:

0.0000243

AC XY:

AN XY:

41172

show subpopulations

African (AFR)

AF:

0.0000455

AC:

AN:

21968

American (AMR)

AF:

0.00

AC:

AN:

7544

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2542

East Asian (EAS)

AF:

0.00

AC:

AN:

3518

South Asian (SAS)

AF:

0.00

AC:

AN:

2414

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2704

Middle Eastern (MID)

AF:

0.00

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

46986

Other (OTH)

AF:

0.00

AC:

AN:

1168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.875

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over