Variant 7-100153898-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001008395.4(LAMTOR4):c.234G>A(p.Thr78Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,591,650 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0094 ( 10 hom., cov: 32)

Exomes 𝑓: 0.010 ( 107 hom. )

Consequence

LAMTOR4
NM_001008395.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.270

Variant links:

Genes affected

LAMTOR4 (HGNC:33772): (late endosomal/lysosomal adaptor, MAPK and MTOR activator 4) Contributes to guanyl-nucleotide exchange factor activity and molecular adaptor activity. Involved in several processes, including cellular response to amino acid stimulus; positive regulation of TOR signaling; and protein localization to lysosome. Located in lysosome. Part of Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]

LAMTOR4 links:

LAMTOR4 (HGNC:):

LAMTOR4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 7-100153898-G-A is Benign according to our data. Variant chr7-100153898-G-A is described in ClinVar as [Benign]. Clinvar id is 2657739.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.27 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMTOR4	NM_001008395.4 linkuse as main transcript	c.234G>A	p.Thr78Thr	synonymous_variant	4/4	ENST00000341942.10	NP_001008396.1	Q0VGL1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAMTOR4	ENST00000341942.10 linkuse as main transcript	c.234G>A	p.Thr78Thr	synonymous_variant	4/4	1	NM_001008395.4	ENSP00000343118.5		Q0VGL1

Frequencies

GnomAD3 genomes

AF:

0.00938

AC:

1428

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00203

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0131

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.0203

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.0125

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.00941

AC:

2023

AN:

215010

Hom.:

AF XY:

0.00977

AC XY:

1124

AN XY:

115060

show subpopulations

Gnomad AFR exome

AF:

0.00179

Gnomad AMR exome

AF:

0.00876

Gnomad ASJ exome

AF:

0.00902

Gnomad EAS exome

AF:

0.0000620

Gnomad SAS exome

AF:

0.00144

Gnomad FIN exome

AF:

0.0219

Gnomad NFE exome

AF:

0.0120

Gnomad OTH exome

AF:

0.0109

GnomAD4 exome

AF:

0.0102

AC:

14711

AN:

1439360

Hom.:

107

Cov.:

AF XY:

0.0101

AC XY:

7230

AN XY:

713564

show subpopulations

Gnomad4 AFR exome

AF:

0.00162

Gnomad4 AMR exome

AF:

0.00865

Gnomad4 ASJ exome

AF:

0.00964

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00155

Gnomad4 FIN exome

AF:

0.0228

Gnomad4 NFE exome

AF:

0.0110

Gnomad4 OTH exome

AF:

0.00908

GnomAD4 genome

AF:

0.00938

AC:

1428

AN:

152290

Hom.:

Cov.:

AF XY:

0.00944

AC XY:

703

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00202

Gnomad4 AMR

AF:

0.0131

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0203

Gnomad4 NFE

AF:

0.0125

Gnomad4 OTH

AF:

0.00993

Alfa

AF:

0.0107

Hom.:

Bravo

AF:

0.00857

Asia WGS

AF:

0.00144

AC:

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

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2024

LAMTOR4: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

8.0

DANN

Benign

0.89

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

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