rs4919611

Variant names:

• chr10-102135182-C-A
• rs4919611
• NM_015062.5:c.153+1961C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-102135182-C-A
• chr10-102135182-C-G
• chr10-102135182-C-T

Variant summary

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

The NM_015062.5(PPRC1):​c.153+1961C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,234 control chromosomes in the GnomAD database, including 62,325 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 0.90 (62325 hom., cov: 31)
• Consequence: PPRC1 NM_015062.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015062.5. 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+1961C>A		intron	N/A	NP_055877.3
	PPRC1	NM_001288728.2		c.-107+1961C>A		intron	N/A	NP_001275657.1
	PPRC1	NM_001288727.2		c.153+1961C>A		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+1961C>A		intron	N/A	ENSP00000278070.2
	PPRC1	ENST00000413464.6	TSL:2	c.153+1961C>A		intron	N/A	ENSP00000399743.2

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137421 AN: 152116 Hom.: 62263 Cov.: 31

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.903 AC: 137541 AN: 152234 Hom.: 62325 Cov.: 31 AF XY: 0.902 AC XY: 67150 AN XY: 74418

African (AFR) AF: 0.967 AC: 40186 AN: 41554

American (AMR) AF: 0.894 AC: 13645 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2720 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4320 AN: 5168

South Asian (SAS) AF: 0.839 AC: 4052 AN: 4828

European-Finnish (FIN) AF: 0.941 AC: 9972 AN: 10598

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59724 AN: 68028

Other (OTH) AF: 0.872 AC: 1844 AN: 2114

Alfa AF: 0.884 Hom.: 62460

Bravo AF: 0.904

Asia WGS AF: 0.873 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		0.74
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: rs4919611; hg19: chr10-103894939;