chr7-28075634-T-C

Variant names:

• chr7-28075634-T-C
• rs2158622
• NM_175061.4:c.116-83653A>G

Variant summary

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

The NM_175061.4(JAZF1):​c.116-83653A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,244 control chromosomes in the GnomAD database, including 63,673 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 0.91 (63673 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.116-83653A>G		intron_variant	Intron 1 of 4	ENST00000283928.10	NP_778231.2
JAZF1	XM_047420024.1	c.116-83653A>G		intron_variant	Intron 1 of 3		XP_047275980.1
JAZF1	XM_047420026.1	c.-77-83653A>G		intron_variant	Intron 1 of 4		XP_047275982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.116-83653A>G		intron_variant	Intron 1 of 4	1	NM_175061.4	ENSP00000283928.5
JAZF1	ENST00000452993.5	n.116-83653A>G		intron_variant	Intron 1 of 4	4		ENSP00000415984.1
JAZF1	ENST00000454041.1	n.171-83653A>G		intron_variant	Intron 1 of 3	5
JAZF1	ENST00000649905.1	n.*157+25985A>G		intron_variant	Intron 2 of 5			ENSP00000497321.1

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138841 AN: 152126 Hom.: 63608 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.913 AC: 138967 AN: 152244 Hom.: 63673 Cov.: 32 AF XY: 0.908 AC XY: 67611 AN XY: 74438

African (AFR) AF: 0.980 AC: 40738 AN: 41556

American (AMR) AF: 0.930 AC: 14218 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3154 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4496 AN: 5190

South Asian (SAS) AF: 0.742 AC: 3575 AN: 4820

European-Finnish (FIN) AF: 0.879 AC: 9304 AN: 10580

Middle Eastern (MID) AF: 0.932 AC: 272 AN: 292

European-Non Finnish (NFE) AF: 0.891 AC: 60621 AN: 68024

Other (OTH) AF: 0.903 AC: 1909 AN: 2114

Alfa AF: 0.900 Hom.: 129743

Bravo AF: 0.923

Asia WGS AF: 0.823 AC: 2858 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		-0.39
Mutation Taster		=99/1	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: rs2158622; hg19: chr7-28115253;