rs10807843

Variant names:

• chr7-27952771-T-C
• rs10807843
• NM_175061.4:c.188+39138A>G

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+39138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,254 control chromosomes in the GnomAD database, including 3,320 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 0.18 (3320 hom., cov: 33)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 8 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=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.188+39138A>G		intron_variant	Intron 2 of 4	ENST00000283928.10	NP_778231.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.188+39138A>G		intron_variant	Intron 2 of 4	1	NM_175061.4	ENSP00000283928.5

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28025 AN: 152136 Hom.: 3318 Cov.: 33

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.184 AC: 28033 AN: 152254 Hom.: 3320 Cov.: 33 AF XY: 0.188 AC XY: 14004 AN XY: 74436

African (AFR) AF: 0.0549 AC: 2281 AN: 41564

American (AMR) AF: 0.228 AC: 3486 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2325 AN: 5172

South Asian (SAS) AF: 0.264 AC: 1275 AN: 4830

European-Finnish (FIN) AF: 0.243 AC: 2572 AN: 10594

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14450 AN: 68008

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.210 Hom.: 1557

Bravo AF: 0.181

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		0.51
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: rs10807843; hg19: chr7-27992390;