7-28149792-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_175061.4(JAZF1):c.115+30671A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,036 control chromosomes in the GnomAD database, including 14,052 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.42 (14052 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.278

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 7-28149792-T-C is Benign according to our data. Variant chr7-28149792-T-C is described in ClinVar as [Benign]. Clinvar id is 1287219.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAZF1	NM_175061.4	c.115+30671A>G		intron_variant		ENST00000283928.10
JAZF1	XM_047420024.1	c.115+30671A>G		intron_variant
JAZF1	XM_047420026.1	c.-78+30038A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1	ENST00000283928.10	c.115+30671A>G		intron_variant		1	NM_175061.4	P1
JAZF1	ENST00000452993.5	c.115+30671A>G		intron_variant, NMD_transcript_variant		4
JAZF1	ENST00000649905.1	c.115+30671A>G		intron_variant, NMD_transcript_variant
JAZF1	ENST00000454041.1	n.170+30671A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63232 AN: 151918 Hom.: 14049 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.416 AC: 63246 AN: 152036 Hom.: 14052 Cov.: 32 AF XY: 0.411 AC XY: 30514 AN XY: 74304

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.422

Alfa AF: 0.480 Hom.: 37416

Bravo AF: 0.406

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 28, 2020

This variant is associated with the following publications: (PMID: 23328127) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.0
Dann	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1635852; hg19: chr7-28189411;