7-27936126-C-T

Position:

• chr7-27936126-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.189-40710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,186 control chromosomes in the GnomAD database, including 3,336 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 0.19 (3336 hom., cov: 33)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.189-40710G>A		intron_variant		ENST00000283928.10	NP_778231.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.189-40710G>A		intron_variant		1	NM_175061.4	ENSP00000283928	P1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28617 AN: 152068 Hom.: 3334 Cov.: 33

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.188 AC: 28619 AN: 152186 Hom.: 3336 Cov.: 33 AF XY: 0.192 AC XY: 14281 AN XY: 74408

Gnomad4 AFR AF: 0.0667

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.198

Alfa AF: 0.217 Hom.: 6829

Bravo AF: 0.186

Asia WGS AF: 0.360 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.73

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: rs17156041; hg19: chr7-27975745;