rs10225163

Positions:

• chr7-27886026-C-G

Variant summary

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

The NM_175061.4(JAZF1):​c.385+9194G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,112 control chromosomes in the GnomAD database, including 21,573 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 0.53 (21573 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAZF1	NM_175061.4	c.385+9194G>C		intron_variant		ENST00000283928.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1	ENST00000283928.10	c.385+9194G>C		intron_variant		1	NM_175061.4	P1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80523 AN: 151994 Hom.: 21541 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.530 AC: 80594 AN: 152112 Hom.: 21573 Cov.: 32 AF XY: 0.525 AC XY: 39051 AN XY: 74332

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.571

Alfa AF: 0.536 Hom.: 2731

Bravo AF: 0.529

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.32

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: rs10225163; hg19: chr7-27925645;