7-28145472-A-G

Position:

• chr7-28145472-A-G

Variant summary

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

The NM_175061.4(JAZF1):​c.115+34991T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,134 control chromosomes in the GnomAD database, including 47,294 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 0.78 (47294 hom., cov: 32)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAZF1	NM_175061.4	c.115+34991T>C		intron_variant		ENST00000283928.10
JAZF1	XM_047420024.1	c.115+34991T>C		intron_variant
JAZF1	XM_047420026.1	c.-78+34358T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1	ENST00000283928.10	c.115+34991T>C		intron_variant		1	NM_175061.4	P1
JAZF1	ENST00000452993.5	c.115+34991T>C		intron_variant, NMD_transcript_variant		4
JAZF1	ENST00000649905.1	c.115+34991T>C		intron_variant, NMD_transcript_variant
JAZF1	ENST00000454041.1	n.170+34991T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119049 AN: 152016 Hom.: 47236 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.783 AC: 119163 AN: 152134 Hom.: 47294 Cov.: 32 AF XY: 0.782 AC XY: 58175 AN XY: 74356

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.764

Alfa AF: 0.742 Hom.: 98975

Bravo AF: 0.803

Asia WGS AF: 0.889 AC: 3094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
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: rs849141; hg19: chr7-28185091;