chr7-28156794-G-A

Variant names:

• chr7-28156794-G-A
• rs849135
• NM_175061.4:c.115+23669C>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+23669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,900 control chromosomes in the GnomAD database, including 12,981 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 0.39 (12981 hom., cov: 31)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 99 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 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.115+23669C>T		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.115+23669C>T		intron	N/A	ENSP00000283928.5	Q86VZ6-1
	JAZF1	ENST00000900291.1		c.115+23669C>T		intron	N/A	ENSP00000570350.1
	JAZF1	ENST00000919133.1		c.115+23669C>T		intron	N/A	ENSP00000589192.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59655 AN: 151782 Hom.: 12981 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.393 AC: 59661 AN: 151900 Hom.: 12981 Cov.: 31 AF XY: 0.385 AC XY: 28569 AN XY: 74216

African (AFR) AF: 0.252 AC: 10449 AN: 41434

American (AMR) AF: 0.414 AC: 6324 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1878 AN: 3472

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5178

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4810

European-Finnish (FIN) AF: 0.445 AC: 4669 AN: 10500

Middle Eastern (MID) AF: 0.403 AC: 116 AN: 288

European-Non Finnish (NFE) AF: 0.496 AC: 33691 AN: 67932

Other (OTH) AF: 0.401 AC: 847 AN: 2110

Alfa AF: 0.442 Hom.: 22020

Bravo AF: 0.384

Asia WGS AF: 0.148 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs849135; hg19: chr7-28196413;