7-27944162-C-T

Position:

• chr7-27944162-C-T

Variant summary

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

The ENST00000283928.10(JAZF1):​c.188+47747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,140 control chromosomes in the GnomAD database, including 3,218 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 0.18 (3218 hom., cov: 32)
• Consequence: JAZF1 ENST00000283928.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAZF1	NM_175061.4	c.188+47747G>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+47747G>A		intron_variant		1	NM_175061.4	ENSP00000283928	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27706 AN: 152022 Hom.: 3216 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.182 AC: 27711 AN: 152140 Hom.: 3218 Cov.: 32 AF XY: 0.186 AC XY: 13850 AN XY: 74394

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.196

Alfa AF: 0.161 Hom.: 726

Bravo AF: 0.179

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.6
DANN	Benign	0.49

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: rs11982766; hg19: chr7-27983781;