rs4722750

Positions:

• chr7-27964579-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175061.4(JAZF1):​c.188+27330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,536 control chromosomes in the GnomAD database, including 1,357 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 0.13 (1357 hom., cov: 30)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAZF1	NM_175061.4	c.188+27330G>A		intron_variant		ENST00000283928.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1	ENST00000283928.10	c.188+27330G>A		intron_variant		1	NM_175061.4	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18963 AN: 151420 Hom.: 1356 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.125 AC: 18970 AN: 151536 Hom.: 1357 Cov.: 30 AF XY: 0.126 AC XY: 9306 AN XY: 74042

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0907

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0979 Hom.: 1380

Bravo AF: 0.126

Asia WGS AF: 0.137 AC: 478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs4722750; hg19: chr7-28004198;