Variant chr11-72094686-T-TGA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_145309.6(LRRC51):c.289-256_289-255dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 722,600 control chromosomes in the GnomAD database, including 4,448 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1265 hom., cov: 30)

Exomes 𝑓: 0.088 ( 3183 hom. )

Consequence

LRRC51
NM_145309.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.605

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-72094686-T-TGA is Benign according to our data. Variant chr11-72094686-T-TGA is described in ClinVar as [Benign]. Clinvar id is 1258396.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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.289-256_289-255dup		intron_variant		ENST00000289488.8
LRTOMT	NM_001145309.4 linkuse as main transcript	c.-115-256_-115-255dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC51	ENST00000289488.8 linkuse as main transcript	c.289-256_289-255dup		intron_variant		1	NM_145309.6	P1	Q96E66-1

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17284

AN:

152030

Hom.:

1264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.0899

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0675

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0549

Gnomad OTH

AF:

0.0966

GnomAD4 exome

AF:

0.0881

AC:

50229

AN:

570452

Hom.:

3183

Cov.:

AF XY:

0.0904

AC XY:

27816

AN XY:

307572

show subpopulations

Gnomad4 AFR exome

AF:

0.180

Gnomad4 AMR exome

AF:

0.146

Gnomad4 ASJ exome

AF:

0.0895

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.154

Gnomad4 FIN exome

AF:

0.0689

Gnomad4 NFE exome

AF:

0.0544

Gnomad4 OTH exome

AF:

0.0883

GnomAD4 genome

AF:

0.114

AC:

17312

AN:

152148

Hom.:

1265

Cov.:

AF XY:

0.119

AC XY:

8825

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.0899

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.0675

Gnomad4 NFE

AF:

0.0549

Gnomad4 OTH

AF:

0.0946

Alfa

AF:

0.0836

Hom.:

Bravo

AF:

0.121

Asia WGS

AF:

0.177

AC:

617

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

Jan 28, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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