rs215

Variant names:

• chr7-27895635-A-C
• rs215
• NM_175061.4:c.189-219T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-27895635-A-C
• chr7-27895635-A-G
• chr7-27895635-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.189-219T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,178 control chromosomes in the GnomAD database, including 69,073 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 0.95 (69073 hom., cov: 30)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175061.4. 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.189-219T>G		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.189-219T>G		intron	N/A	ENSP00000283928.5
	JAZF1	ENST00000427814.5	TSL:1	c.147-219T>G		intron	N/A	ENSP00000388302.1
	JAZF1	ENST00000447620.5	TSL:4	c.117-219T>G		intron	N/A	ENSP00000415096.1

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144756 AN: 152060 Hom.: 69008 Cov.: 30

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.952 AC: 144880 AN: 152178 Hom.: 69073 Cov.: 30 AF XY: 0.955 AC XY: 71000 AN XY: 74384

African (AFR) AF: 0.987 AC: 41001 AN: 41528

American (AMR) AF: 0.926 AC: 14155 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3118 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5148 AN: 5152

South Asian (SAS) AF: 0.983 AC: 4734 AN: 4818

European-Finnish (FIN) AF: 0.970 AC: 10278 AN: 10594

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63321 AN: 68010

Other (OTH) AF: 0.921 AC: 1946 AN: 2114

Alfa AF: 0.936 Hom.: 53677

Bravo AF: 0.950

Asia WGS AF: 0.984 AC: 3421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		0.38
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: rs215; hg19: chr7-27935254;