11-36417447-C-T

Variant summary

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

The NM_001160167.2(PRR5L):c.246-1808C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,960 control chromosomes in the GnomAD database, including 11,579 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 0.39 (11579 hom., cov: 32)
• Consequence: PRR5L NM_001160167.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

Genes affected

PRR5L (HGNC:25878): (proline rich 5 like) Enables ubiquitin protein ligase binding activity. Involved in several processes, including TORC2 signaling; positive regulation of mRNA catabolic process; and regulation of fibroblast migration. Part of TORC2 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRR5L	NM_001160167.2	c.246-1808C>T		intron_variant		ENST00000530639.6
PRR5L	NM_001160168.2	c.3-1808C>T		intron_variant
PRR5L	NM_001160169.1	c.246-1808C>T		intron_variant
PRR5L	NM_024841.5	c.246-1808C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR5L	ENST00000530639.6	c.246-1808C>T		intron_variant		2	NM_001160167.2	P1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58473 AN: 151842 Hom.: 11560 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.385 AC: 58524 AN: 151960 Hom.: 11579 Cov.: 32 AF XY: 0.387 AC XY: 28776 AN XY: 74266

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.373

Alfa AF: 0.375 Hom.: 1631

Bravo AF: 0.390

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.1
Dann	Benign	0.77

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: rs10836555; hg19: chr11-36438997;