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GeneBe

rs864745

Variant summary

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

The NM_175061.4(JAZF1):c.115+39526A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,152 control chromosomes in the GnomAD database, including 13,752 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 0.41 ( 13752 hom., cov: 33)

Consequence

JAZF1
NM_175061.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76
Variant links:
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
JAZF1NM_175061.4 linkuse as main transcriptc.115+39526A>G intron_variant ENST00000283928.10
JAZF1XM_047420024.1 linkuse as main transcriptc.115+39526A>G intron_variant
JAZF1XM_047420026.1 linkuse as main transcriptc.-78+38893A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
JAZF1ENST00000283928.10 linkuse as main transcriptc.115+39526A>G intron_variant 1 NM_175061.4 P1Q86VZ6-1
JAZF1ENST00000452993.5 linkuse as main transcriptc.115+39526A>G intron_variant, NMD_transcript_variant 4
JAZF1ENST00000649905.1 linkuse as main transcriptc.116-39133A>G intron_variant, NMD_transcript_variant
JAZF1ENST00000454041.1 linkuse as main transcriptn.170+39526A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.410
AC:
62282
AN:
152034
Hom.:
13752
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.255
Gnomad AMI
AF:
0.482
Gnomad AMR
AF:
0.424
Gnomad ASJ
AF:
0.543
Gnomad EAS
AF:
0.226
Gnomad SAS
AF:
0.270
Gnomad FIN
AF:
0.497
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.503
Gnomad OTH
AF:
0.424
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.409
AC:
62286
AN:
152152
Hom.:
13752
Cov.:
33
AF XY:
0.404
AC XY:
30082
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.254
Gnomad4 AMR
AF:
0.424
Gnomad4 ASJ
AF:
0.543
Gnomad4 EAS
AF:
0.226
Gnomad4 SAS
AF:
0.270
Gnomad4 FIN
AF:
0.497
Gnomad4 NFE
AF:
0.503
Gnomad4 OTH
AF:
0.418
Alfa
AF:
0.473
Hom.:
21983
Bravo
AF:
0.398
Asia WGS
AF:
0.249
AC:
870
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.059
Dann
Benign
0.41

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: rs864745; hg19: chr7-28180556; API