rs10225163

Variant names:

• chr7-27886026-C-G
• rs10225163
• NM_175061.4:c.385+9194G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.97).
• 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 rank	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.385+9194G>C		intron_variant	Intron 3 of 4	ENST00000283928.10	NP_778231.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.385+9194G>C		intron_variant	Intron 3 of 4	1	NM_175061.4	ENSP00000283928.5

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

African (AFR) AF: 0.467 AC: 19371 AN: 41504

American (AMR) AF: 0.495 AC: 7571 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2463 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2505 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4818

European-Finnish (FIN) AF: 0.519 AC: 5474 AN: 10556

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38826 AN: 67984

Other (OTH) AF: 0.571 AC: 1208 AN: 2114

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
PhyloP100		0.016
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: rs10225163; hg19: chr7-27925645;