7-27964402-C-T

Position:

• chr7-27964402-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175061.4(JAZF1):​c.188+27507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,196 control chromosomes in the GnomAD database, including 67,923 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 0.94 (67923 hom., cov: 30)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.188+27507G>A		intron_variant		ENST00000283928.10	NP_778231.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.188+27507G>A		intron_variant		1	NM_175061.4	ENSP00000283928	P1

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143549 AN: 152078 Hom.: 67862 Cov.: 30

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.944 AC: 143669 AN: 152196 Hom.: 67923 Cov.: 30 AF XY: 0.947 AC XY: 70445 AN XY: 74416

Gnomad4 AFR AF: 0.985

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.922

Alfa AF: 0.926 Hom.: 31446

Bravo AF: 0.944

Asia WGS AF: 0.983 AC: 3415 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs995367; hg19: chr7-28004021;