15-41828144-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -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. 13/21 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

Publications

7 publications found

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:34449): (JMJD7-PLA2G4B readthrough) This locus represents naturally-occurring readthrough transcription between the neighboring jumonji domain containing 7 (JMJD7) and phospholipase A2, group IVB (cytosolic) (PLA2G4B) genes. Readthrough transcripts encode fusion proteins that share amino acid sequence with each individual gene product, including a partial JmjC domain and downstream C2 and phospholipase A2 domains. Alternatively spliced transcript variants have been observed. [provided by RefSeq, Oct 2013]

JMJD7-PLA2G4B links:

ENSG00000250379 (HGNC:):

ENSG00000250379 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114632.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
JMJD7	NM_001114632.2	MANE Select	c.20A>G	p.Glu7Gly	missense	Exon 1 of 8	NP_001108104.1	P0C870
JMJD7-PLA2G4B	NM_005090.4		c.20A>G	p.Glu7Gly	missense	Exon 1 of 25	NP_005081.1
JMJD7-PLA2G4B	NM_001198588.2		c.20A>G	p.Glu7Gly	missense	Exon 1 of 24	NP_001185517.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
JMJD7	ENST00000397299.9	TSL:1 MANE Select	c.20A>G	p.Glu7Gly	missense	Exon 1 of 8	ENSP00000380467.4	P0C870
JMJD7-PLA2G4B	ENST00000382448.8	TSL:2	c.20A>G	p.Glu7Gly	missense	Exon 1 of 25	ENSP00000371886.4
JMJD7-PLA2G4B	ENST00000342159.6	TSL:2	c.20A>G	p.Glu7Gly	missense	Exon 1 of 24	ENSP00000342785.4

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

GnomAD2 exomes

AF:

0.0323

AC:

4660

AN:

144378

AF XY:

0.0335

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 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

African (AFR)

AF:

0.00645

AC:

167

AN:

25892

American (AMR)

AF:

0.0238

AC:

458

AN:

19274

Ashkenazi Jewish (ASJ)

AF:

0.0184

AC:

404

AN:

21974

East Asian (EAS)

AF:

0.000192

AC:

AN:

31244

South Asian (SAS)

AF:

0.00650

AC:

438

AN:

67380

European-Finnish (FIN)

AF:

0.0395

AC:

1975

AN:

50012

Middle Eastern (MID)

AF:

0.00477

AC:

AN:

4404

European-Non Finnish (NFE)

AF:

0.0526

AC:

55446

AN:

1054108

Other (OTH)

AF:

0.0402

AC:

2180

AN:

54296

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

3428

6856

10284

13712

17140

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2134

4268

6402

8536

10670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0305

AC:

4643

AN:

152048

Hom.:

104

Cov.:

AF XY:

0.0290

AC XY:

2156

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.00798

AC:

331

AN:

41456

American (AMR)

AF:

0.0247

AC:

378

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3470

East Asian (EAS)

AF:

0.000194

AC:

AN:

5156

South Asian (SAS)

AF:

0.00374

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.0392

AC:

415

AN:

10598

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0496

AC:

3372

AN:

67940

Other (OTH)

AF:

0.0284

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

234

468

703

937

1171

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0408

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

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

JMJD7-PLA2G4B-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.69

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.084

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.73

FATHMM_MKL

Benign

0.24

LIST_S2

Benign

0.39

MetaRNN

Benign

0.0023

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.55

PhyloP100

1.0

PrimateAI

Uncertain

0.59

PROVEAN

Benign

-1.1

REVEL

Benign

0.040

Sift

Benign

0.090

Sift4G

Uncertain

0.025

Polyphen

0.0

Vest4

0.16

MPC

0.022

ClinPred

0.021

GERP RS

1.3

PromoterAI

0.022

Neutral

(source)

Varity_R

0.19

gMVP

0.57

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over