7-28149464-T-G

Variant names:

• chr7-28149464-T-G
• rs1029534
• NM_175061.4:c.115+30999A>C

Variant summary

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

The ENST00000283928.10(JAZF1):​c.115+30999A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 151,900 control chromosomes in the GnomAD database, including 46,358 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 0.78 (46358 hom., cov: 29)
• Consequence: JAZF1 ENST00000283928.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 16 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000283928.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	NM_175061.4	MANE Select	c.115+30999A>C		intron	N/A	NP_778231.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	ENST00000283928.10	TSL:1 MANE Select	c.115+30999A>C		intron	N/A	ENSP00000283928.5
	JAZF1	ENST00000452993.5	TSL:4	n.115+30999A>C		intron	N/A	ENSP00000415984.1
	JAZF1	ENST00000454041.1	TSL:5	n.170+30999A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117662 AN: 151782 Hom.: 46301 Cov.: 29

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.775 AC: 117775 AN: 151900 Hom.: 46358 Cov.: 29 AF XY: 0.774 AC XY: 57482 AN XY: 74222

African (AFR) AF: 0.878 AC: 36401 AN: 41446

American (AMR) AF: 0.824 AC: 12573 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2825 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5030 AN: 5146

South Asian (SAS) AF: 0.760 AC: 3646 AN: 4796

European-Finnish (FIN) AF: 0.649 AC: 6837 AN: 10536

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47985 AN: 67940

Other (OTH) AF: 0.756 AC: 1596 AN: 2110

Alfa AF: 0.745 Hom.: 62724

Bravo AF: 0.798

Asia WGS AF: 0.888 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.1
DANN	Benign	0.84
PhyloP100		-0.33
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: rs1029534; hg19: chr7-28189083;