16-11553676-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001136472.2(LITAF):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 0.0123 in 1,614,036 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 13 hom., cov: 32)

Exomes 𝑓: 0.013 ( 140 hom. )

Consequence

LITAF
NM_001136472.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -6.45

Variant links:

Genes affected

LITAF (HGNC:16841): (lipopolysaccharide induced TNF factor) Lipopolysaccharide is a potent stimulator of monocytes and macrophages, causing secretion of tumor necrosis factor-alpha (TNF-alpha) and other inflammatory mediators. This gene encodes lipopolysaccharide-induced TNF-alpha factor, which is a DNA-binding protein and can mediate the TNF-alpha expression by direct binding to the promoter region of the TNF-alpha gene. The transcription of this gene is induced by tumor suppressor p53 and has been implicated in the p53-induced apoptotic pathway. Mutations in this gene cause Charcot-Marie-Tooth disease type 1C (CMT1C) and may be involved in the carcinogenesis of extramammary Paget's disease (EMPD). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2014]

LITAF links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 16-11553676-C-T is Benign according to our data. Variant chr16-11553676-C-T is described in ClinVar as [Benign]. Clinvar id is 220753.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-11553676-C-T is described in Lovd as [Benign]. Variant chr16-11553676-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-6.45 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00998 (1520/152248) while in subpopulation NFE AF= 0.015 (1023/68018). AF 95% confidence interval is 0.0143. There are 13 homozygotes in gnomad4. There are 680 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1520 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LITAF	NM_001136472.2 link	c.234G>A	p.Thr78Thr	synonymous_variant	Exon 3 of 4	ENST00000622633.5	NP_001129944.1	Q99732-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LITAF	ENST00000622633.5 link	c.234G>A	p.Thr78Thr	synonymous_variant	Exon 3 of 4	1	NM_001136472.2	ENSP00000483114.1		Q99732-1

Frequencies

GnomAD3 genomes

AF:

0.0100

AC:

1521

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00256

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0111

Gnomad ASJ

AF:

0.0306

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.00302

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0150

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0103

AC:

2575

AN:

250860

Hom.:

AF XY:

0.0108

AC XY:

1466

AN XY:

135600

show subpopulations

Gnomad AFR exome

AF:

0.00271

Gnomad AMR exome

AF:

0.00654

Gnomad ASJ exome

AF:

0.0242

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00906

Gnomad FIN exome

AF:

0.00250

Gnomad NFE exome

AF:

0.0147

Gnomad OTH exome

AF:

0.0105

GnomAD4 exome

AF:

0.0126

AC:

18355

AN:

1461788

Hom.:

140

Cov.:

AF XY:

0.0127

AC XY:

9249

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.00287

Gnomad4 AMR exome

AF:

0.00798

Gnomad4 ASJ exome

AF:

0.0264

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.00978

Gnomad4 FIN exome

AF:

0.00320

Gnomad4 NFE exome

AF:

0.0137

Gnomad4 OTH exome

AF:

0.0135

GnomAD4 genome

AF:

0.00998

AC:

1520

AN:

152248

Hom.:

Cov.:

AF XY:

0.00913

AC XY:

680

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00255

Gnomad4 AMR

AF:

0.0111

Gnomad4 ASJ

AF:

0.0306

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00829

Gnomad4 FIN

AF:

0.00302

Gnomad4 NFE

AF:

0.0150

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.0152

Hom.:

Bravo

AF:

0.0102

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.0161

EpiControl

AF:

0.0187

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Charcot-Marie-Tooth disease type 1C

Benign:3

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 16, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

LITAF: BP4, BP7, BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Charcot-Marie-Tooth disease

Benign:1

Molecular Genetics Laboratory, London Health Sciences Centre

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.10

DANN

Benign

0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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