7-28136686-G-A

Variant names:

• chr7-28136686-G-A
• rs917117
• NM_175061.4:c.115+43777C>T

Variant summary

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

The NM_175061.4(JAZF1):​c.115+43777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,148 control chromosomes in the GnomAD database, including 7,957 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 0.30 (7957 hom., cov: 33)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 26 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 (EAS) allele frequency at 95% confidence interval = 0.725 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	NM_175061.4	MANE Select	c.115+43777C>T		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+43777C>T		intron	N/A	ENSP00000283928.5
	JAZF1	ENST00000452993.5	TSL:4	n.115+43777C>T		intron	N/A	ENSP00000415984.1
	JAZF1	ENST00000454041.1	TSL:5	n.170+43777C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44925 AN: 152030 Hom.: 7921 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.296 AC: 45009 AN: 152148 Hom.: 7957 Cov.: 33 AF XY: 0.301 AC XY: 22383 AN XY: 74382

African (AFR) AF: 0.371 AC: 15408 AN: 41484

American (AMR) AF: 0.376 AC: 5753 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3855 AN: 5176

South Asian (SAS) AF: 0.488 AC: 2355 AN: 4824

European-Finnish (FIN) AF: 0.152 AC: 1606 AN: 10600

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14155 AN: 67984

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.242 Hom.: 8681

Bravo AF: 0.319

Asia WGS AF: 0.613 AC: 2130 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	1.6
DANN	Benign	0.57
PhyloP100		-0.37
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: rs917117; hg19: chr7-28176305;