rs10486567

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_175061(JAZF1):c.189-41528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152004 control chromosomes in the gnomAD Genomes database, including 7718 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 0.29 ( 7718 hom., cov: 33)

Consequence

JAZF1
NM_175061 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.568

Links

JAZF1 (HGNC:28917):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAZF1	NM_175061.4 linkuse as main transcript	c.189-41528C>T		intron_variant		ENST00000283928.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1	ENST00000283928.10 linkuse as main transcript	c.189-41528C>T		intron_variant		1	NM_175061.4	P1	Q86VZ6-1

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44361

AN:

152004

Hom.:

7718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.874

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.292

Alfa

AF:

0.251

Hom.:

10205

Bravo

AF:

0.308

Asia WGS

AF:

0.565

AC:

1964

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

Cadd

Benign

Dann

Benign

0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over