chr7-28136686-G-A

Position:

• chr7-28136686-G-A

Variant summary

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

The NM_175061.4(JAZF1):​c.115+43777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,148 control chromosomes in the GnomAD database, including 7,957 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 0.30 (7957 hom., cov: 33)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAZF1	NM_175061.4	c.115+43777C>T		intron_variant		ENST00000283928.10
JAZF1	XM_047420024.1	c.115+43777C>T		intron_variant
JAZF1	XM_047420026.1	c.-78+43144C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1	ENST00000283928.10	c.115+43777C>T		intron_variant		1	NM_175061.4	P1
JAZF1	ENST00000452993.5	c.115+43777C>T		intron_variant, NMD_transcript_variant		4
JAZF1	ENST00000649905.1	c.116-34882C>T		intron_variant, NMD_transcript_variant
JAZF1	ENST00000454041.1	n.170+43777C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44925 AN: 152030 Hom.: 7921 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.296 AC: 45009 AN: 152148 Hom.: 7957 Cov.: 33 AF XY: 0.301 AC XY: 22383 AN XY: 74382

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.290

Alfa AF: 0.243 Hom.: 6558

Bravo AF: 0.319

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.57

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: rs917117; hg19: chr7-28176305;