chr10-102134948-G-C

Variant names:

• chr10-102134948-G-C
• rs4917960
• NM_015062.5:c.153+1727G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000278070.7(PPRC1):​c.153+1727G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,080 control chromosomes in the GnomAD database, including 27,020 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 0.56 (27020 hom., cov: 32)
• Consequence: PPRC1 ENST00000278070.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 1 publications found

Genes affected

PPRC1 (HGNC:30025): (PPARG related coactivator 1) The protein encoded by this gene is similar to PPAR-gamma coactivator 1 (PPARGC1/PGC-1), a protein that can activate mitochondrial biogenesis in part through a direct interaction with nuclear respiratory factor 1 (NRF1). This protein has been shown to interact with NRF1. It is thought to be a functional relative of PPAR-gamma coactivator 1 that activates mitochondrial biogenesis through NRF1 in response to proliferative signals. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000278070.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPRC1	NM_015062.5	MANE Select	c.153+1727G>C		intron	N/A	NP_055877.3
	PPRC1	NM_001288728.2		c.-107+1727G>C		intron	N/A	NP_001275657.1
	PPRC1	NM_001288727.2		c.153+1727G>C		intron	N/A	NP_001275656.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPRC1	ENST00000278070.7	TSL:1 MANE Select	c.153+1727G>C		intron	N/A	ENSP00000278070.2
	PPRC1	ENST00000413464.6	TSL:2	c.153+1727G>C		intron	N/A	ENSP00000399743.2

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85239 AN: 151962 Hom.: 26961 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.561 AC: 85357 AN: 152080 Hom.: 27020 Cov.: 32 AF XY: 0.556 AC XY: 41362 AN XY: 74344

African (AFR) AF: 0.870 AC: 36095 AN: 41496

American (AMR) AF: 0.481 AC: 7341 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3597 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2012 AN: 4824

European-Finnish (FIN) AF: 0.415 AC: 4387 AN: 10562

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28881 AN: 67982

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.288 Hom.: 584

Bravo AF: 0.581

Asia WGS AF: 0.601 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4917960; hg19: chr10-103894705;