chr5-149822705-C-A

Position:

• chr5-149822705-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133263.4(PPARGC1B):​c.252+2099C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,280 control chromosomes in the GnomAD database, including 532 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 0.075 (532 hom., cov: 32)
• Consequence: PPARGC1B NM_133263.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1B	NM_133263.4	c.252+2099C>A		intron_variant		ENST00000309241.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPARGC1B	ENST00000309241.10	c.252+2099C>A		intron_variant		1	NM_133263.4	P2
PPARGC1B	ENST00000360453.8	c.252+2099C>A		intron_variant		1		A2
PPARGC1B	ENST00000394320.7	c.252+2099C>A		intron_variant		1		A2
PPARGC1B	ENST00000403750.5	c.177+2099C>A		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11430 AN: 152162 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.0678

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0751 AC: 11439 AN: 152280 Hom.: 532 Cov.: 32 AF XY: 0.0743 AC XY: 5531 AN XY: 74460

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0514

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0583

Gnomad4 OTH AF: 0.0666

Alfa AF: 0.0327 Hom.: 80

Bravo AF: 0.0785

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.52

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

Other links and lift over

dbSNP: rs1078324; hg19: chr5-149202268;