rs10491360

Variant summary

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

The NM_133263.4(PPARGC1B):​c.79-2181T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,272 control chromosomes in the GnomAD database, including 1,361 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 0.11 ( 1361 hom., cov: 33)

Consequence

PPARGC1B
NM_133263.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.414
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPARGC1BNM_133263.4 linkuse as main transcriptc.79-2181T>C 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.79-2181T>C intron_variant 1 NM_133263.4 ENSP00000312649.5 Q86YN6-1
PPARGC1BENST00000394320.7 linkuse as main transcriptc.79-2181T>C intron_variant 1 ENSP00000377855.3 Q86YN6-3
PPARGC1BENST00000360453.8 linkuse as main transcriptc.79-2181T>C intron_variant 1 ENSP00000353638.4 Q86YN6-5
PPARGC1BENST00000403750.5 linkuse as main transcriptc.4-2181T>C intron_variant 2 ENSP00000384403.1 Q86YN6-6

Frequencies

GnomAD3 genomes
AF:
0.106
AC:
16071
AN:
152154
Hom.:
1347
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.218
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.164
Gnomad ASJ
AF:
0.0320
Gnomad EAS
AF:
0.0878
Gnomad SAS
AF:
0.0374
Gnomad FIN
AF:
0.0625
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0433
Gnomad OTH
AF:
0.0884
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.106
AC:
16136
AN:
152272
Hom.:
1361
Cov.:
33
AF XY:
0.106
AC XY:
7863
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.218
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.0320
Gnomad4 EAS
AF:
0.0875
Gnomad4 SAS
AF:
0.0377
Gnomad4 FIN
AF:
0.0625
Gnomad4 NFE
AF:
0.0432
Gnomad4 OTH
AF:
0.0908
Alfa
AF:
0.0704
Hom.:
162
Bravo
AF:
0.124
Asia WGS
AF:
0.0690
AC:
238
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.0
DANN
Benign
0.84

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: rs10491360; hg19: chr5-149197815; API