7-27964402-C-T

Variant names:

• chr7-27964402-C-T
• rs995367
• NM_175061.4:c.188+27507G>A

Variant summary

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

The NM_175061.4(JAZF1):​c.188+27507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,196 control chromosomes in the GnomAD database, including 67,923 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 0.94 (67923 hom., cov: 30)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.188+27507G>A		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.188+27507G>A		intron	N/A	ENSP00000283928.5
	JAZF1	ENST00000427814.5	TSL:1	c.146+27507G>A		intron	N/A	ENSP00000388302.1
	JAZF1	ENST00000447620.5	TSL:4	c.116+27507G>A		intron	N/A	ENSP00000415096.1

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143549 AN: 152078 Hom.: 67862 Cov.: 30

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.944 AC: 143669 AN: 152196 Hom.: 67923 Cov.: 30 AF XY: 0.947 AC XY: 70445 AN XY: 74416

African (AFR) AF: 0.985 AC: 40901 AN: 41536

American (AMR) AF: 0.936 AC: 14310 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3115 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5142 AN: 5144

South Asian (SAS) AF: 0.974 AC: 4699 AN: 4822

European-Finnish (FIN) AF: 0.961 AC: 10189 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62232 AN: 68014

Other (OTH) AF: 0.922 AC: 1947 AN: 2112

Alfa AF: 0.925 Hom.: 35047

Bravo AF: 0.944

Asia WGS AF: 0.983 AC: 3415 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.79
PhyloP100		-0.46
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: rs995367; hg19: chr7-28004021;