rs741581

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_133263.4(PPARGC1B):​c.252+2616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 152,218 control chromosomes in the GnomAD database, including 366 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 366 hom., cov: 32)

Consequence

PPARGC1B
NM_133263.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13
Variant links:
Genes affected
PPARGC1B (HGNC:30022): (PPARG coactivator 1 beta) The protein encoded by this gene stimulates the activity of several transcription factors and nuclear receptors, including estrogen receptor alpha, nuclear respiratory factor 1, and glucocorticoid receptor. The encoded protein may be involved in fat oxidation, non-oxidative glucose metabolism, and the regulation of energy expenditure. This protein is downregulated in prediabetic and type 2 diabetes mellitus patients. Certain allelic variations in this gene increase the risk of the development of obesity. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0914 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPARGC1BNM_133263.4 linkuse as main transcriptc.252+2616G>A intron_variant ENST00000309241.10 NP_573570.3 Q86YN6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPARGC1BENST00000309241.10 linkuse as main transcriptc.252+2616G>A intron_variant 1 NM_133263.4 ENSP00000312649.5 Q86YN6-1
PPARGC1BENST00000394320.7 linkuse as main transcriptc.252+2616G>A intron_variant 1 ENSP00000377855.3 Q86YN6-3
PPARGC1BENST00000360453.8 linkuse as main transcriptc.252+2616G>A intron_variant 1 ENSP00000353638.4 Q86YN6-5
PPARGC1BENST00000403750.5 linkuse as main transcriptc.177+2616G>A intron_variant 2 ENSP00000384403.1 Q86YN6-6

Frequencies

GnomAD3 genomes
AF:
0.0631
AC:
9596
AN:
152100
Hom.:
366
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0244
Gnomad AMI
AF:
0.0626
Gnomad AMR
AF:
0.0686
Gnomad ASJ
AF:
0.0798
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0230
Gnomad FIN
AF:
0.0524
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0933
Gnomad OTH
AF:
0.0793
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0630
AC:
9594
AN:
152218
Hom.:
366
Cov.:
32
AF XY:
0.0600
AC XY:
4464
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.0243
Gnomad4 AMR
AF:
0.0685
Gnomad4 ASJ
AF:
0.0798
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0234
Gnomad4 FIN
AF:
0.0524
Gnomad4 NFE
AF:
0.0933
Gnomad4 OTH
AF:
0.0785
Alfa
AF:
0.0830
Hom.:
188
Bravo
AF:
0.0630
Asia WGS
AF:
0.0120
AC:
43
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
12
DANN
Benign
0.67

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.

Other links and lift over

dbSNP: rs741581; hg19: chr5-149202785; API