rs10486570

Variant names:

• chr7-27994497-A-G
• rs10486570
• NM_175061.4:c.116-2516T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-27994497-A-G
• chr7-27994497-A-T

Variant summary

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

The NM_175061.4(JAZF1):​c.116-2516T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0963 in 152,082 control chromosomes in the GnomAD database, including 781 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 0.096 (781 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.116-2516T>C		intron_variant	Intron 1 of 4	ENST00000283928.10	NP_778231.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.116-2516T>C		intron_variant	Intron 1 of 4	1	NM_175061.4	ENSP00000283928.5

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14648 AN: 151966 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0963 AC: 14642 AN: 152082 Hom.: 781 Cov.: 32 AF XY: 0.0976 AC XY: 7254 AN XY: 74358

African (AFR) AF: 0.107 AC: 4445 AN: 41476

American (AMR) AF: 0.0706 AC: 1080 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3470

East Asian (EAS) AF: 0.136 AC: 704 AN: 5182

South Asian (SAS) AF: 0.145 AC: 698 AN: 4822

European-Finnish (FIN) AF: 0.121 AC: 1275 AN: 10558

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0892 AC: 6065 AN: 67962

Other (OTH) AF: 0.0733 AC: 155 AN: 2116

Alfa AF: 0.0862 Hom.: 1023

Bravo AF: 0.0912

Asia WGS AF: 0.129 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.82
PhyloP100		0.14
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: rs10486570; hg19: chr7-28034116;