Variant 15-41835222-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001114632.2(JMJD7):c.471G>T(p.Leu157=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000835 in 1,597,494 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 6 hom., cov: 33)

Exomes 𝑓: 0.00046 ( 3 hom. )

Consequence

JMJD7
NM_001114632.2 splice_region, synonymous

Scores

Splicing: ADA: 0.0001044

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.294

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 15-41835222-G-T is Benign according to our data. Variant chr15-41835222-G-T is described in ClinVar as [Benign]. Clinvar id is 787425.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-41835222-G-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.294 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000464 (671/1445184) while in subpopulation AFR AF= 0.0166 (555/33448). AF 95% confidence interval is 0.0155. There are 3 homozygotes in gnomad4_exome. There are 292 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
JMJD7	NM_001114632.2 linkuse as main transcript	c.471G>T	p.Leu157=	splice_region_variant, synonymous_variant	3/8	ENST00000397299.9
JMJD7-PLA2G4B	NM_005090.4 linkuse as main transcript	c.471G>T	p.Leu157=	splice_region_variant, synonymous_variant	3/25
JMJD7-PLA2G4B	NM_001198588.2 linkuse as main transcript	c.471G>T	p.Leu157=	splice_region_variant, synonymous_variant	3/24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
JMJD7	ENST00000397299.9 linkuse as main transcript	c.471G>T	p.Leu157=	splice_region_variant, synonymous_variant	3/8	1	NM_001114632.2	P1
JMJD7	ENST00000408047.5 linkuse as main transcript	c.174G>T	p.Leu58=	splice_region_variant, synonymous_variant	2/7	5
JMJD7	ENST00000431823.1 linkuse as main transcript	c.174G>T	p.Leu58=	splice_region_variant, synonymous_variant	4/7	5

Frequencies

GnomAD3 genomes

AF:

0.00432

AC:

658

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0148

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00106

AC:

239

AN:

225134

Hom.:

AF XY:

0.000832

AC XY:

103

AN XY:

123736

show subpopulations

Gnomad AFR exome

AF:

0.0144

Gnomad AMR exome

AF:

0.000473

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:

0.0000294

Gnomad OTH exome

AF:

0.000874

GnomAD4 exome

AF:

0.000464

AC:

671

AN:

1445184

Hom.:

Cov.:

AF XY:

0.000406

AC XY:

292

AN XY:

719188

show subpopulations

Gnomad4 AFR exome

AF:

0.0166

Gnomad4 AMR exome

AF:

0.000609

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000207

Gnomad4 OTH exome

AF:

0.000997

GnomAD4 genome

AF:

0.00435

AC:

663

AN:

152310

Hom.:

Cov.:

AF XY:

0.00407

AC XY:

303

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.0149

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000103

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.000637

Hom.:

Bravo

AF:

0.00500

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 08, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.2

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00010

dbscSNV1_RF

Benign

0.0

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