chr5-38845303-CAAAAAAAA-C

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)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSMR-DTNR_109951.1 linkn.162+357_162+364delTTTTTTTT intron_variant Intron 1 of 3
OSMR-DTNR_171676.1 linkn.102+357_102+364delTTTTTTTT intron_variant Intron 1 of 2
OSMR-DTNR_171677.1 linkn.102+357_102+364delTTTTTTTT intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSMR-DTENST00000512519.2 linkn.165+357_165+364delTTTTTTTT intron_variant Intron 1 of 1 2
OSMR-DTENST00000513480.2 linkn.107+357_107+364delTTTTTTTT intron_variant Intron 1 of 3 4
OSMR-DTENST00000636516.3 linkn.151+357_151+364delTTTTTTTT intron_variant Intron 1 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.0000111
AC:
1
AN:
89698
Hom.:
0
Cov.:
0
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:
1
AN:
89678
Hom.:
0
Cov.:
0
AF XY:
0.0000243
AC XY:
1
AN XY:
41172
show subpopulations
African (AFR)
AF:
0.0000455
AC:
1
AN:
21968
American (AMR)
AF:
0.00
AC:
0
AN:
7544
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2542
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3518
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2414
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2704
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
156
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
46986
Other (OTH)
AF:
0.00
AC:
0
AN:
1168
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.875
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.23

Splicing

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

Publications

Other links and lift over

dbSNP: rs5867434; hg19: chr5-38845405; API