Variant rs76502784 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_203446.3(SYNJ1):c.479+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 1,603,016 control chromosomes in the GnomAD database, including 1,822 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.034 ( 110 hom., cov: 32)

Exomes 𝑓: 0.046 ( 1712 hom. )

Consequence

SYNJ1
NM_203446.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.30

Variant links:

Genes affected

SYNJ1 (HGNC:11503): (synaptojanin 1) This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

SYNJ1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 21-32699829-T-C is Benign according to our data. Variant chr21-32699829-T-C is described in ClinVar as [Benign]. Clinvar id is 478364.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNJ1	NM_203446.3 linkuse as main transcript	c.479+9A>G		intron_variant		ENST00000674351.1	NP_982271.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNJ1	ENST00000674351.1 linkuse as main transcript	c.479+9A>G		intron_variant			NM_203446.3	ENSP00000501530		O43426-2

Frequencies

GnomAD3 genomes

AF:

0.0336

AC:

5111

AN:

152008

Hom.:

110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.0750

Gnomad SAS

AF:

0.0357

Gnomad FIN

AF:

0.0314

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0462

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.0377

AC:

9181

AN:

243770

Hom.:

194

AF XY:

0.0379

AC XY:

4999

AN XY:

132068

show subpopulations

Gnomad AFR exome

AF:

0.0155

Gnomad AMR exome

AF:

0.0132

Gnomad ASJ exome

AF:

0.0190

Gnomad EAS exome

AF:

0.0746

Gnomad SAS exome

AF:

0.0366

Gnomad FIN exome

AF:

0.0380

Gnomad NFE exome

AF:

0.0440

Gnomad OTH exome

AF:

0.0356

GnomAD4 exome

AF:

0.0461

AC:

66837

AN:

1450890

Hom.:

1712

Cov.:

AF XY:

0.0455

AC XY:

32825

AN XY:

720824

show subpopulations

Gnomad4 AFR exome

AF:

0.0142

Gnomad4 AMR exome

AF:

0.0134

Gnomad4 ASJ exome

AF:

0.0192

Gnomad4 EAS exome

AF:

0.0706

Gnomad4 SAS exome

AF:

0.0363

Gnomad4 FIN exome

AF:

0.0373

Gnomad4 NFE exome

AF:

0.0497

Gnomad4 OTH exome

AF:

0.0398

GnomAD4 genome

AF:

0.0336

AC:

5107

AN:

152126

Hom.:

110

Cov.:

AF XY:

0.0328

AC XY:

2439

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.0155

Gnomad4 AMR

AF:

0.0211

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.0751

Gnomad4 SAS

AF:

0.0353

Gnomad4 FIN

AF:

0.0314

Gnomad4 NFE

AF:

0.0462

Gnomad4 OTH

AF:

0.0242

Alfa

AF:

0.0388

Hom.:

Bravo

AF:

0.0316

Asia WGS

AF:

0.0480

AC:

169

AN:

3478

EpiCase

AF:

0.0405

EpiControl

AF:

0.0408

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 09, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Early-onset Parkinson disease 20;C4479313:Developmental and epileptic encephalopathy, 53

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.5

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over