Variant chr11-72088622-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_145309.6(LRRC51):c.-56+242A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 570,294 control chromosomes in the GnomAD database, including 235,000 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.89 ( 60160 hom., cov: 31)

Exomes 𝑓: 0.91 ( 174840 hom. )

Consequence

LRRC51
NM_145309.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0240

Variant links:

Genes affected

LRRC51 (HGNC:55526): (leucine rich repeat containing 51) This gene belongs to the leucine-rich repeat containing family. The encoded protein contains a transmembrane domain and two leucine-rich repeat domains. Unlike in mouse and other mammals, readthrough transcription is observed in primates between this gene and the adjacent transmembrane O-methyltransferase (Tomt) gene. Previously, this locus was annotated as a single gene representing the readthrough transcripts as well as the two different transcript species that encoded different proteins. It has since been split into three genes, including the two stand-alone genes and a third gene representing the readthrough transcription. [provided by RefSeq, Feb 2022]

LRRC51 links:

LRTOMT (HGNC:):

LRTOMT links:

LAMTOR1 (HGNC:26068): (late endosomal/lysosomal adaptor, MAPK and MTOR activator 1) Enables GTPase binding activity. Contributes to guanyl-nucleotide exchange factor activity and molecular adaptor activity. Involved in several processes, including cholesterol homeostasis; positive regulation of TOR signaling; and regulation of cholesterol transport. Located in lysosome. Part of Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]

LAMTOR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 11-72088622-A-C is Benign according to our data. Variant chr11-72088622-A-C is described in ClinVar as [Benign]. Clinvar id is 1251059.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC51	NM_145309.6 linkuse as main transcript	c.-56+242A>C		intron_variant		ENST00000289488.8
LRTOMT	NM_001145309.4 linkuse as main transcript	c.-459+242A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC51	ENST00000289488.8 linkuse as main transcript	c.-56+242A>C		intron_variant		1	NM_145309.6	P1	Q96E66-1

Frequencies

GnomAD3 genomes

AF:

0.887

AC:

134898

AN:

152020

Hom.:

60128

Cov.:

show subpopulations

Gnomad AFR

AF:

0.819

Gnomad AMI

AF:

0.943

Gnomad AMR

AF:

0.829

Gnomad ASJ

AF:

0.910

Gnomad EAS

AF:

0.769

Gnomad SAS

AF:

0.839

Gnomad FIN

AF:

0.932

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.945

Gnomad OTH

AF:

0.906

GnomAD4 exome

AF:

0.912

AC:

381563

AN:

418156

Hom.:

174840

Cov.:

AF XY:

0.910

AC XY:

200092

AN XY:

219948

show subpopulations

Gnomad4 AFR exome

AF:

0.823

Gnomad4 AMR exome

AF:

0.846

Gnomad4 ASJ exome

AF:

0.911

Gnomad4 EAS exome

AF:

0.779

Gnomad4 SAS exome

AF:

0.844

Gnomad4 FIN exome

AF:

0.931

Gnomad4 NFE exome

AF:

0.946

Gnomad4 OTH exome

AF:

0.913

GnomAD4 genome

AF:

0.887

AC:

134988

AN:

152138

Hom.:

60160

Cov.:

AF XY:

0.882

AC XY:

65610

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.818

Gnomad4 AMR

AF:

0.829

Gnomad4 ASJ

AF:

0.910

Gnomad4 EAS

AF:

0.770

Gnomad4 SAS

AF:

0.839

Gnomad4 FIN

AF:

0.932

Gnomad4 NFE

AF:

0.945

Gnomad4 OTH

AF:

0.908

Alfa

AF:

0.909

Hom.:

3021

Bravo

AF:

0.880

Asia WGS

AF:

0.823

AC:

2859

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.63

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over