rs6968704

Variant names:

• chr7-27927365-C-T
• rs6968704
• NM_175061.4:c.189-31949G>A

Variant summary

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

The NM_175061.4(JAZF1):​c.189-31949G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,024 control chromosomes in the GnomAD database, including 10,716 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 0.36 (10716 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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.189-31949G>A		intron	N/A	NP_778231.2	Q86VZ6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	ENST00000283928.10	TSL:1 MANE Select	c.189-31949G>A		intron	N/A	ENSP00000283928.5	Q86VZ6-1
	JAZF1	ENST00000427814.5	TSL:1	c.147-31949G>A		intron	N/A	ENSP00000388302.1	H0Y403
	JAZF1	ENST00000900291.1		c.189-31949G>A		intron	N/A	ENSP00000570350.1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54071 AN: 151906 Hom.: 10706 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.356 AC: 54103 AN: 152024 Hom.: 10716 Cov.: 32 AF XY: 0.364 AC XY: 27015 AN XY: 74312

African (AFR) AF: 0.311 AC: 12889 AN: 41438

American (AMR) AF: 0.457 AC: 6983 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3464

East Asian (EAS) AF: 0.911 AC: 4710 AN: 5170

South Asian (SAS) AF: 0.423 AC: 2038 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3999 AN: 10566

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21269 AN: 67980

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.326 Hom.: 5213

Bravo AF: 0.367

Asia WGS AF: 0.644 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.42
PhyloP100		-1.4
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: rs6968704; hg19: chr7-27966984;