7-28103871-G-T

Position:

• chr7-28103871-G-T

Variant summary

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

The NM_175061.4(JAZF1):​c.115+76592C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,074 control chromosomes in the GnomAD database, including 48,090 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 0.79 (48090 hom., cov: 31)
• Consequence: JAZF1 NM_175061.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

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 (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.115+76592C>A		intron_variant		ENST00000283928.10	NP_778231.2
JAZF1	XM_047420024.1	c.115+76592C>A		intron_variant			XP_047275980.1
JAZF1	XM_047420026.1	c.-78+75959C>A		intron_variant			XP_047275982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAZF1	ENST00000283928.10	c.115+76592C>A		intron_variant		1	NM_175061.4	ENSP00000283928	P1
JAZF1	ENST00000452993.5	c.115+76592C>A		intron_variant, NMD_transcript_variant		4		ENSP00000415984
JAZF1	ENST00000649905.1	c.116-2067C>A		intron_variant, NMD_transcript_variant				ENSP00000497321
JAZF1	ENST00000454041.1	n.170+76592C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120434 AN: 151956 Hom.: 48044 Cov.: 31

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.793 AC: 120539 AN: 152074 Hom.: 48090 Cov.: 31 AF XY: 0.790 AC XY: 58736 AN XY: 74324

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.791

Alfa AF: 0.755 Hom.: 46109

Bravo AF: 0.801

Asia WGS AF: 0.757 AC: 2631 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	0.64
DANN	Benign	0.65

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: rs2158623; hg19: chr7-28143490;