Variant 22-46218377-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005036.6(PPARA):c.484C>G(p.Leu162Val) variant causes a missense change. The variant allele was found at a frequency of 0.0573 in 1,614,008 control chromosomes in the GnomAD database, including 3,094 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.042 ( 172 hom., cov: 30)

Exomes 𝑓: 0.059 ( 2922 hom. )

Consequence

PPARA
NM_005036.6 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 6.00

Variant links:

Genes affected

PPARA (HGNC:9232): (peroxisome proliferator activated receptor alpha) Peroxisome proliferators include hypolipidemic drugs, herbicides, leukotriene antagonists, and plasticizers; this term arises because they induce an increase in the size and number of peroxisomes. Peroxisomes are subcellular organelles found in plants and animals that contain enzymes for respiration and for cholesterol and lipid metabolism. The action of peroxisome proliferators is thought to be mediated via specific receptors, called PPARs, which belong to the steroid hormone receptor superfamily. PPARs affect the expression of target genes involved in cell proliferation, cell differentiation and in immune and inflammation responses. Three closely related subtypes (alpha, beta/delta, and gamma) have been identified. This gene encodes the subtype PPAR-alpha, which is a nuclear transcription factor. Multiple alternatively spliced transcript variants have been described for this gene, although the full-length nature of only two has been determined. [provided by RefSeq, Jul 2008]

PPARA 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=0.00670588).

BP6

Variant 22-46218377-C-G is Benign according to our data. Variant chr22-46218377-C-G is described in ClinVar as [Benign]. Clinvar id is 13701.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARA	NM_005036.6 linkuse as main transcript	c.484C>G	p.Leu162Val	missense_variant	6/9	ENST00000407236.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPARA	ENST00000407236.6 linkuse as main transcript	c.484C>G	p.Leu162Val	missense_variant	6/9	1	NM_005036.6	P1	Q07869-1
PPARA	ENST00000402126.1 linkuse as main transcript	c.484C>G	p.Leu162Val	missense_variant	4/7	1		P1	Q07869-1
PPARA	ENST00000493286.1 linkuse as main transcript	n.694C>G		non_coding_transcript_exon_variant	5/6	1

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6425

AN:

152108

Hom.:

173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0124

Gnomad AMI

AF:

0.0714

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0228

Gnomad FIN

AF:

0.0300

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0643

Gnomad OTH

AF:

0.0606

GnomAD3 exomes

AF:

0.0434

AC:

10923

AN:

251492

Hom.:

316

AF XY:

0.0433

AC XY:

5889

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.0105

Gnomad AMR exome

AF:

0.0402

Gnomad ASJ exome

AF:

0.0429

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0245

Gnomad FIN exome

AF:

0.0325

Gnomad NFE exome

AF:

0.0626

Gnomad OTH exome

AF:

0.0572

GnomAD4 exome

AF:

0.0588

AC:

86009

AN:

1461782

Hom.:

2922

Cov.:

AF XY:

0.0578

AC XY:

42060

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.00923

Gnomad4 AMR exome

AF:

0.0429

Gnomad4 ASJ exome

AF:

0.0415

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0251

Gnomad4 FIN exome

AF:

0.0339

Gnomad4 NFE exome

AF:

0.0677

Gnomad4 OTH exome

AF:

0.0529

GnomAD4 genome

AF:

0.0422

AC:

6417

AN:

152226

Hom.:

172

Cov.:

AF XY:

0.0399

AC XY:

2972

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0124

Gnomad4 AMR

AF:

0.0503

Gnomad4 ASJ

AF:

0.0395

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0224

Gnomad4 FIN

AF:

0.0300

Gnomad4 NFE

AF:

0.0642

Gnomad4 OTH

AF:

0.0586

Alfa

AF:

0.0569

Hom.:

Bravo

AF:

0.0436

TwinsUK

AF:

0.0680

AC:

252

ALSPAC

AF:

0.0693

AC:

267

ESP6500AA

AF:

0.0127

AC:

ESP6500EA

AF:

0.0624

AC:

537

ExAC

AF:

0.0425

AC:

5155

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.0678

EpiControl

AF:

0.0649

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Hyperapobetalipoproteinemia, susceptibility to

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jan 01, 2004

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Uncertain

0.086

BayesDel_noAF

Pathogenic

0.40

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.68

D;D;D

Eigen

Uncertain

0.26

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.88

D;.;.

MetaRNN

Benign

0.0067

T;T;T

MetaSVM

Uncertain

0.056

MutationAssessor

Benign

1.7

L;L;L

MutationTaster

Benign

1.0

D;D;D;D;D

PrimateAI

Uncertain

0.72

PROVEAN

Benign

-1.8

N;N;N

REVEL

Pathogenic

0.67

Sift

Uncertain

0.0080

D;D;D

Sift4G

Uncertain

0.052

T;T;T

Polyphen

0.17

B;B;B

Vest4

0.36

ClinPred

0.021

GERP RS

5.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.20

gMVP

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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