NM_175061.4:c.116-8316T>C

Variant names:

• chr7-28000297-A-G
• rs6945134
• NM_175061.4:c.116-8316T>C

Variant summary

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

The NM_175061.4(JAZF1):​c.116-8316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,096 control chromosomes in the GnomAD database, including 6,265 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 0.24 (6265 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 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.116-8316T>C		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.116-8316T>C		intron	N/A	ENSP00000283928.5	Q86VZ6-1
	JAZF1	ENST00000900291.1		c.116-8316T>C		intron	N/A	ENSP00000570350.1
	JAZF1	ENST00000919133.1		c.116-8316T>C		intron	N/A	ENSP00000589192.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35932 AN: 151978 Hom.: 6247 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0974

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.237 AC: 35991 AN: 152096 Hom.: 6265 Cov.: 32 AF XY: 0.229 AC XY: 17068 AN XY: 74390

African (AFR) AF: 0.484 AC: 20047 AN: 41438

American (AMR) AF: 0.173 AC: 2637 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4824

European-Finnish (FIN) AF: 0.0974 AC: 1033 AN: 10604

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.155 AC: 10571 AN: 67982

Other (OTH) AF: 0.233 AC: 493 AN: 2114

Alfa AF: 0.184 Hom.: 6108

Bravo AF: 0.257

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		0.21
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: rs6945134; hg19: chr7-28039916;