Variant X-108150100-T-TG details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_052936.5(ATG4A):c.815-49dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 1,181,727 control chromosomes in the GnomAD database, including 87,204 homozygotes. There are 167,479 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.50 ( 10710 hom., 15801 hem., cov: 0)

Exomes 𝑓: 0.45 ( 76494 hom. 151678 hem. )

Consequence

ATG4A
NM_052936.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.895

Variant links:

Genes affected

ATG4A (HGNC:16489): (autophagy related 4A cysteine peptidase) Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. [provided by RefSeq, Mar 2016]

ATG4A links:

ATG4A (HGNC:):

ATG4A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-108150100-T-TG is Benign according to our data. Variant chrX-108150100-T-TG is described in ClinVar as [Benign]. Clinvar id is 2688250.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG4A	NM_052936.5 linkuse as main transcript	c.815-49dupG		intron_variant		ENST00000372232.8	NP_443168.2	Q8WYN0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG4A	ENST00000372232.8 linkuse as main transcript	c.815-49dupG		intron_variant		1	NM_052936.5	ENSP00000361306.3		Q8WYN0-1

Frequencies

GnomAD3 genomes

AF:

0.497

AC:

54845

AN:

110422

Hom.:

10704

Cov.:

AF XY:

0.482

AC XY:

15768

AN XY:

32702

show subpopulations

Gnomad AFR

AF:

0.678

Gnomad AMI

AF:

0.801

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.584

Gnomad MID

AF:

0.378

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.431

GnomAD4 exome

AF:

0.446

AC:

477318

AN:

1071256

Hom.:

76494

Cov.:

AF XY:

0.443

AC XY:

151678

AN XY:

342436

show subpopulations

Gnomad4 AFR exome

AF:

0.679

Gnomad4 AMR exome

AF:

0.195

Gnomad4 ASJ exome

AF:

0.346

Gnomad4 EAS exome

AF:

0.104

Gnomad4 SAS exome

AF:

0.329

Gnomad4 FIN exome

AF:

0.588

Gnomad4 NFE exome

AF:

0.465

Gnomad4 OTH exome

AF:

0.428

GnomAD4 genome

AF:

0.497

AC:

54879

AN:

110471

Hom.:

10710

Cov.:

AF XY:

0.482

AC XY:

15801

AN XY:

32761

show subpopulations

Gnomad4 AFR

AF:

0.678

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.584

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.435

Alfa

AF:

0.509

Hom.:

3686

Bravo

AF:

0.481

Asia WGS

AF:

0.240

AC:

604

AN:

2505

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 31% of patients studied by a panel of primary immunodeficiencies. Number of patients: 29. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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