rs10486572

Variant names:

• chr7-28038505-T-A
• rs10486572
• NM_175061.4:c.116-46524A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000283928.10(JAZF1):​c.116-46524A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 152,266 control chromosomes in the GnomAD database, including 411 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 0.055 (411 hom., cov: 33)
• Consequence: JAZF1 ENST00000283928.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 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

LOC105375208 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000283928.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	NM_175061.4	MANE Select	c.116-46524A>T		intron	N/A	NP_778231.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1	ENST00000283928.10	TSL:1 MANE Select	c.116-46524A>T		intron	N/A	ENSP00000283928.5
	JAZF1	ENST00000430432.5	TSL:4	c.16+33113A>T		intron	N/A	ENSP00000387976.1
	JAZF1	ENST00000452993.5	TSL:4	n.116-46524A>T		intron	N/A	ENSP00000415984.1

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8367 AN: 152148 Hom.: 407 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.0537

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0355

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

GnomAD4 genome AF: 0.0551 AC: 8386 AN: 152266 Hom.: 411 Cov.: 33 AF XY: 0.0555 AC XY: 4130 AN XY: 74456

African (AFR) AF: 0.127 AC: 5259 AN: 41550

American (AMR) AF: 0.0243 AC: 372 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 39 AN: 3466

East Asian (EAS) AF: 0.0534 AC: 277 AN: 5186

South Asian (SAS) AF: 0.0816 AC: 394 AN: 4828

European-Finnish (FIN) AF: 0.0323 AC: 343 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0238 AC: 1619 AN: 68026

Other (OTH) AF: 0.0351 AC: 74 AN: 2108

Alfa AF: 0.0445 Hom.: 36

Bravo AF: 0.0548

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.2
DANN	Benign	0.74
PhyloP100		-0.16
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: rs10486572; hg19: chr7-28078124;