rs10486567
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_175061.4(JAZF1):c.189-41528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,122 control chromosomes in the GnomAD database, including 7,730 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 0.29 ( 7730 hom., cov: 33)
Consequence
JAZF1
NM_175061.4 intron
NM_175061.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.568
Genes affected
JAZF1 (HGNC:28917): (JAZF zinc finger 1) This gene encodes a nuclear protein with three C2H2-type zinc fingers, and functions as a transcriptional repressor. Chromosomal aberrations involving this gene are associated with endometrial stromal tumors. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.292 AC: 44361AN: 152004Hom.: 7718 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
44361
AN:
152004
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.292 AC: 44396AN: 152122Hom.: 7730 Cov.: 33 AF XY: 0.299 AC XY: 22242AN XY: 74382 show subpopulations
GnomAD4 genome
AF:
AC:
44396
AN:
152122
Hom.:
Cov.:
33
AF XY:
AC XY:
22242
AN XY:
74382
Gnomad4 AFR
AF:
AC:
0.28516
AN:
0.28516
Gnomad4 AMR
AF:
AC:
0.406213
AN:
0.406213
Gnomad4 ASJ
AF:
AC:
0.305876
AN:
0.305876
Gnomad4 EAS
AF:
AC:
0.874181
AN:
0.874181
Gnomad4 SAS
AF:
AC:
0.313148
AN:
0.313148
Gnomad4 FIN
AF:
AC:
0.264639
AN:
0.264639
Gnomad4 NFE
AF:
AC:
0.228741
AN:
0.228741
Gnomad4 OTH
AF:
AC:
0.294034
AN:
0.294034
Heterozygous variant carriers
0
1489
2977
4466
5954
7443
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
436
872
1308
1744
2180
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1964
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at