Variant 1-227733552-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000620518.5(JMJD4):c.684C>T(p.Tyr228Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00842 in 1,606,598 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0080 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0085 ( 72 hom. )

Consequence

JMJD4
ENST00000620518.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.226

Variant links:

Genes affected

JMJD4 (HGNC:25724): (jumonji domain containing 4) Enables 2-oxoglutarate-dependent dioxygenase activity. Involved in positive regulation of translational termination and protein hydroxylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

JMJD4 links:

SNAP47 (HGNC:30669): (synaptosome associated protein 47) Predicted to enable SNAP receptor activity and syntaxin binding activity. Predicted to be involved in synaptic vesicle fusion to presynaptic active zone membrane and synaptic vesicle priming. Predicted to act upstream of or within long-term synaptic potentiation. Colocalizes with BLOC-1 complex. [provided by Alliance of Genome Resources, Apr 2022]

SNAP47 links:

SNAP47 (HGNC:):

SNAP47 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 1-227733552-G-A is Benign according to our data. Variant chr1-227733552-G-A is described in ClinVar as [Benign]. Clinvar id is 778255.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.226 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JMJD4	NM_023007.3 linkuse as main transcript	c.684C>T	p.Tyr228Tyr	synonymous_variant	4/6	ENST00000620518.5	NP_075383.3	Q9H9V9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JMJD4	ENST00000620518.5 linkuse as main transcript	c.684C>T	p.Tyr228Tyr	synonymous_variant	4/6	1	NM_023007.3	ENSP00000477669.1		A0A087WT84

Frequencies

GnomAD3 genomes

AF:

0.00797

AC:

1213

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00219

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0124

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.0252

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00930

Gnomad OTH

AF:

0.00812

GnomAD3 exomes

AF:

0.00895

AC:

2152

AN:

240360

Hom.:

AF XY:

0.00860

AC XY:

1127

AN XY:

130994

show subpopulations

Gnomad AFR exome

AF:

0.00245

Gnomad AMR exome

AF:

0.00876

Gnomad ASJ exome

AF:

0.00127

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.000332

Gnomad FIN exome

AF:

0.0261

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.0123

GnomAD4 exome

AF:

0.00847

AC:

12321

AN:

1454254

Hom.:

Cov.:

AF XY:

0.00815

AC XY:

5899

AN XY:

723476

show subpopulations

Gnomad4 AFR exome

AF:

0.00176

Gnomad4 AMR exome

AF:

0.00858

Gnomad4 ASJ exome

AF:

0.000739

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000373

Gnomad4 FIN exome

AF:

0.0246

Gnomad4 NFE exome

AF:

0.00910

Gnomad4 OTH exome

AF:

0.00758

GnomAD4 genome

AF:

0.00796

AC:

1213

AN:

152344

Hom.:

Cov.:

AF XY:

0.00855

AC XY:

637

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00219

Gnomad4 AMR

AF:

0.0124

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.0252

Gnomad4 NFE

AF:

0.00930

Gnomad4 OTH

AF:

0.00803

Alfa

AF:

0.00759

Hom.:

Bravo

AF:

0.00615

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00774

EpiControl

AF:

0.00945

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.5

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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