15-41828144-A-G

Position:

chr15-41828144-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001114632.2(JMJD7):c.20A>G(p.Glu7Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 1,480,632 control chromosomes in the GnomAD database, including 1,709 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.031 ( 104 hom., cov: 32)

Exomes 𝑓: 0.046 ( 1605 hom. )

Consequence

JMJD7
NM_001114632.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

JMJD7 (HGNC:34397): (jumonji domain containing 7) This gene encodes a highly conserved protein with a JmjC domain, which are part of the cupin metalloenzyme superfamily. JmjC proteins may function as 2-oxoglutarate-Fe(II)-dependent dioxygenases. Most tissues also express read-through transcripts from this gene into the downstream phospholipase A2, group IVB (cytosolic) gene, some of which may encode fusion proteins combining the N-terminus of this protein with the phospholipase A2, group IVB protein. [provided by RefSeq, Jul 2008]

JMJD7 links:

JMJD7-PLA2G4B (HGNC:):

JMJD7-PLA2G4B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023448467).

BP6

Variant 15-41828144-A-G is Benign according to our data. Variant chr15-41828144-A-G is described in ClinVar as [Benign]. Clinvar id is 3056209.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
JMJD7	NM_001114632.2 linkuse as main transcript	c.20A>G	p.Glu7Gly	missense_variant	1/8	ENST00000397299.9	NP_001108104.1
JMJD7-PLA2G4B	NM_005090.4 linkuse as main transcript	c.20A>G	p.Glu7Gly	missense_variant	1/25		NP_005081.1
JMJD7-PLA2G4B	NM_001198588.2 linkuse as main transcript	c.20A>G	p.Glu7Gly	missense_variant	1/24		NP_001185517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
JMJD7	ENST00000397299.9 linkuse as main transcript	c.20A>G	p.Glu7Gly	missense_variant	1/8	1	NM_001114632.2	ENSP00000380467	P1
JMJD7	ENST00000408047.5 linkuse as main transcript	c.-200A>G		5_prime_UTR_variant	1/7	5		ENSP00000384174
JMJD7	ENST00000431823.1 linkuse as main transcript	c.-386A>G		5_prime_UTR_variant	1/7	5		ENSP00000399600
JMJD7	ENST00000405106.2 linkuse as main transcript	n.32A>G		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes

AF:

0.0305

AC:

4641

AN:

151930

Hom.:

104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00801

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0247

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00373

Gnomad FIN

AF:

0.0392

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0287

GnomAD3 exomes

AF:

0.0323

AC:

4660

AN:

144378

Hom.:

118

AF XY:

0.0335

AC XY:

2765

AN XY:

82552

show subpopulations

Gnomad AFR exome

AF:

0.00783

Gnomad AMR exome

AF:

0.0185

Gnomad ASJ exome

AF:

0.0163

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00612

Gnomad FIN exome

AF:

0.0378

Gnomad NFE exome

AF:

0.0463

Gnomad OTH exome

AF:

0.0384

GnomAD4 exome

AF:

0.0460

AC:

61095

AN:

1328584

Hom.:

1605

Cov.:

AF XY:

0.0448

AC XY:

29312

AN XY:

654728

show subpopulations

Gnomad4 AFR exome

AF:

0.00645

Gnomad4 AMR exome

AF:

0.0238

Gnomad4 ASJ exome

AF:

0.0184

Gnomad4 EAS exome

AF:

0.000192

Gnomad4 SAS exome

AF:

0.00650

Gnomad4 FIN exome

AF:

0.0395

Gnomad4 NFE exome

AF:

0.0526

Gnomad4 OTH exome

AF:

0.0402

GnomAD4 genome

AF:

0.0305

AC:

4643

AN:

152048

Hom.:

104

Cov.:

AF XY:

0.0290

AC XY:

2156

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.00798

Gnomad4 AMR

AF:

0.0247

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00374

Gnomad4 FIN

AF:

0.0392

Gnomad4 NFE

AF:

0.0496

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0431

Hom.:

Bravo

AF:

0.0295

ESP6500AA

AF:

0.00955

AC:

ESP6500EA

AF:

0.0422

AC:

362

ExAC

AF:

0.0286

AC:

3449

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

JMJD7-PLA2G4B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 06, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.084

T;.;.

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.73

FATHMM_MKL

Benign

0.24

LIST_S2

Benign

0.39

T;T;T

MetaRNN

Benign

0.0023

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.55

N;.;.

MutationTaster

Benign

1.0

D;N;N;N;N

PrimateAI

Uncertain

0.59

PROVEAN

Benign

-1.1

N;N;N

REVEL

Benign

0.040

Sift

Benign

0.090

T;D;D

Sift4G

Uncertain

0.025

D;D;D

Polyphen

0.0

B;.;.

Vest4

0.16

MPC

0.022

ClinPred

0.021

GERP RS

1.3

Varity_R

0.19

gMVP

0.57

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

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