11-36417447-C-T

Variant names:

• chr11-36417447-C-T
• rs10836555
• NM_001160167.2:c.246-1808C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001160167.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR5L	NM_001160167.2	MANE Select	c.246-1808C>T		intron	N/A	NP_001153639.1	Q6MZQ0-1
	PRR5L	NM_024841.5		c.246-1808C>T		intron	N/A	NP_079117.3
	PRR5L	NM_001160168.2		c.3-1808C>T		intron	N/A	NP_001153640.1	Q6MZQ0-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR5L	ENST00000530639.6	TSL:2 MANE Select	c.246-1808C>T		intron	N/A	ENSP00000435050.1	Q6MZQ0-1
	PRR5L	ENST00000378867.7	TSL:1	c.246-1808C>T		intron	N/A	ENSP00000368144.3	Q6MZQ0-1
	PRR5L	ENST00000869229.1		c.246-1808C>T		intron	N/A	ENSP00000539287.1

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

African (AFR) AF: 0.432 AC: 17901 AN: 41438

American (AMR) AF: 0.358 AC: 5479 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3348 AN: 5154

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4810

European-Finnish (FIN) AF: 0.332 AC: 3500 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23918 AN: 67944

Other (OTH) AF: 0.373 AC: 789 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.77
PhyloP100		-0.13
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: rs10836555; hg19: chr11-36438997;