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rs5867434

chr5-38845303-CAAAAAAAA-Cchr5-38845303-CAAAAAAAA-CAchr5-38845303-CAAAAAAAA-CAAAchr5-38845303-CAAAAAAAA-CAAAAchr5-38845303-CAAAAAAAA-CAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAAAAAAAchr5-38845303-CAAAAAAAA-CAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NR_109951.1(OSMR-DT):n.162+357_162+364del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 89,678 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
NR_109951.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228
Variant links:
Genes affected
OSMR-DT (HGNC:50296): (OSMR divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OSMR-DTNR_109951.1 linkuse as main transcriptn.162+357_162+364del intron_variant, non_coding_transcript_variant
OSMR-DTNR_171676.1 linkuse as main transcriptn.102+357_102+364del intron_variant, non_coding_transcript_variant
OSMR-DTNR_171677.1 linkuse as main transcriptn.102+357_102+364del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OSMR-DTENST00000662290.1 linkuse as main transcriptn.126+357_126+364del intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000112
AC:
1
AN:
89678
Hom.:
0
Cov.:
0
AF XY:
0.0000243
AC XY:
1
AN XY:
41172
show subpopulations
Gnomad4 AFR
AF:
0.0000455
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5867434; hg19: chr5-38845405; API