chr5-38845303-CA-C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000512519.2(OSMR-DT):​n.165+364delT 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 0.029 ( 180 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)

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 (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0293
AC:
2627
AN:
89640
Hom.:
181
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00666
Gnomad AMI
AF:
0.00885
Gnomad AMR
AF:
0.0203
Gnomad ASJ
AF:
0.0122
Gnomad EAS
AF:
0.378
Gnomad SAS
AF:
0.0357
Gnomad FIN
AF:
0.0107
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0169
Gnomad OTH
AF:
0.0458
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0292
AC:
2616
AN:
89620
Hom.:
180
Cov.:
0
AF XY:
0.0313
AC XY:
1287
AN XY:
41142
show subpopulations
African (AFR)
AF:
0.00665
AC:
146
AN:
21958
American (AMR)
AF:
0.0203
AC:
153
AN:
7544
Ashkenazi Jewish (ASJ)
AF:
0.0122
AC:
31
AN:
2542
East Asian (EAS)
AF:
0.377
AC:
1318
AN:
3496
South Asian (SAS)
AF:
0.0348
AC:
84
AN:
2412
European-Finnish (FIN)
AF:
0.0107
AC:
29
AN:
2702
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
156
European-Non Finnish (NFE)
AF:
0.0169
AC:
794
AN:
46966
Other (OTH)
AF:
0.0472
AC:
55
AN:
1166
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.448
Heterozygous variant carriers
0
80
161
241
322
402
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
40
80
120
160
200
<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.:
0

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

Other links and lift over

dbSNP: rs5867434; hg19: chr5-38845405; API