rs4820345

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001360236.2(JOSD1):​c.185+4657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,116 control chromosomes in the GnomAD database, including 5,278 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5278 hom., cov: 32)

Consequence

JOSD1
NM_001360236.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.500
Variant links:
Genes affected
JOSD1 (HGNC:28953): (Josephin domain containing 1) Predicted to enable thiol-dependent deubiquitinase. Predicted to be involved in protein deubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
JOSD1NM_001360236.2 linkuse as main transcriptc.185+4657A>G intron_variant ENST00000683374.1 NP_001347165.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
JOSD1ENST00000683374.1 linkuse as main transcriptc.185+4657A>G intron_variant NM_001360236.2 ENSP00000506752 P1

Frequencies

GnomAD3 genomes
AF:
0.252
AC:
38371
AN:
151996
Hom.:
5274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.403
Gnomad AMR
AF:
0.223
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.360
Gnomad SAS
AF:
0.276
Gnomad FIN
AF:
0.334
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.252
AC:
38392
AN:
152116
Hom.:
5278
Cov.:
32
AF XY:
0.254
AC XY:
18905
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.223
Gnomad4 ASJ
AF:
0.288
Gnomad4 EAS
AF:
0.359
Gnomad4 SAS
AF:
0.276
Gnomad4 FIN
AF:
0.334
Gnomad4 NFE
AF:
0.297
Gnomad4 OTH
AF:
0.260
Alfa
AF:
0.266
Hom.:
5172
Bravo
AF:
0.237
Asia WGS
AF:
0.311
AC:
1085
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.77
DANN
Benign
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs4820345; hg19: chr22-39091151; API