Variant 15-41828174-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001114632.2(JMJD7):c.50C>T(p.Pro17Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000428 in 1,493,840 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0023 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00022 ( 1 hom. )

Consequence

JMJD7
NM_001114632.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.05

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00689137).

BP6

Variant 15-41828174-C-T is Benign according to our data. Variant chr15-41828174-C-T is described in ClinVar as [Benign]. Clinvar id is 731633.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
JMJD7	NM_001114632.2 linkuse as main transcript	c.50C>T	p.Pro17Leu	missense_variant	1/8	ENST00000397299.9
JMJD7-PLA2G4B	NM_005090.4 linkuse as main transcript	c.50C>T	p.Pro17Leu	missense_variant	1/25
JMJD7-PLA2G4B	NM_001198588.2 linkuse as main transcript	c.50C>T	p.Pro17Leu	missense_variant	1/24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
JMJD7	ENST00000397299.9 linkuse as main transcript	c.50C>T	p.Pro17Leu	missense_variant	1/8	1	NM_001114632.2	P1
JMJD7	ENST00000408047.5 linkuse as main transcript	c.-170C>T		5_prime_UTR_variant	1/7	5
JMJD7	ENST00000431823.1 linkuse as main transcript	c.-356C>T		5_prime_UTR_variant	1/7	5
JMJD7	ENST00000405106.2 linkuse as main transcript	n.62C>T		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes

AF:

0.00227

AC:

345

AN:

152104

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00811

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000458

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000960

GnomAD3 exomes

AF:

0.000543

AC:

AN:

150972

Hom.:

AF XY:

0.000327

AC XY:

AN XY:

85642

show subpopulations

Gnomad AFR exome

AF:

0.00834

Gnomad AMR exome

AF:

0.000255

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000260

Gnomad OTH exome

AF:

0.000327

GnomAD4 exome

AF:

0.000218

AC:

292

AN:

1341618

Hom.:

Cov.:

AF XY:

0.000208

AC XY:

138

AN XY:

662718

show subpopulations

Gnomad4 AFR exome

AF:

0.00930

Gnomad4 AMR exome

AF:

0.000149

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000113

Gnomad4 OTH exome

AF:

0.000601

GnomAD4 genome

AF:

0.00228

AC:

347

AN:

152222

Hom.:

Cov.:

AF XY:

0.00222

AC XY:

165

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00814

Gnomad4 AMR

AF:

0.000458

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000950

Alfa

AF:

0.000485

Hom.:

Bravo

AF:

0.00276

ESP6500AA

AF:

0.00841

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000671

AC:

Asia WGS

AF:

0.000866

AC:

AN:

3478

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	Jul 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.48

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.41

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0074

T;.;.

Eigen

Benign

-0.075

Eigen_PC

Benign

0.052

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.68

T;T;T

MetaRNN

Benign

0.0069

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

M;.;.

MutationTaster

Benign

0.97

D;D;D;D;D

PrimateAI

Uncertain

0.65

PROVEAN

Benign

-1.3

N;N;N

REVEL

Benign

0.029

Sift

Benign

0.39

T;D;D

Sift4G

Benign

0.66

T;D;T

Polyphen

0.32

B;.;.

Vest4

0.64

MVP

0.12

MPC

0.021

ClinPred

0.065

GERP RS

5.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.34

gMVP

0.58

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