NM_175061.4:c.189-42328A>G

Variant names:

• chr7-27937744-T-C
• rs7808935
• NM_175061.4:c.189-42328A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175061.4(JAZF1):​c.189-42328A>G 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 151,972 control chromosomes in the GnomAD database, including 7,752 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 0.29 (7752 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 20 publications found

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]

JAZF1 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175061.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	NM_175061.4	MANE Select	c.189-42328A>G		intron	N/A	NP_778231.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	ENST00000283928.10	TSL:1 MANE Select	c.189-42328A>G		intron	N/A	ENSP00000283928.5
	JAZF1	ENST00000427814.5	TSL:1	c.147-42328A>G		intron	N/A	ENSP00000388302.1
	JAZF1	ENST00000900291.1		c.189-42328A>G		intron	N/A	ENSP00000570350.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44414 AN: 151856 Hom.: 7740 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.292 AC: 44449 AN: 151972 Hom.: 7752 Cov.: 32 AF XY: 0.300 AC XY: 22252 AN XY: 74262

African (AFR) AF: 0.287 AC: 11875 AN: 41442

American (AMR) AF: 0.406 AC: 6203 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1059 AN: 3462

East Asian (EAS) AF: 0.875 AC: 4522 AN: 5170

South Asian (SAS) AF: 0.316 AC: 1520 AN: 4814

European-Finnish (FIN) AF: 0.264 AC: 2789 AN: 10550

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15580 AN: 67962

Other (OTH) AF: 0.295 AC: 622 AN: 2110

Alfa AF: 0.259 Hom.: 4168

Bravo AF: 0.309

Asia WGS AF: 0.567 AC: 1966 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		-0.011
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7808935; hg19: chr7-27977363;