Variant 12-116576326-G-GA details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001085481.3(MAP1LC3B2):c.*12dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,600,402 control chromosomes in the GnomAD database, including 56,546 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 5036 hom., cov: 22)

Exomes 𝑓: 0.26 ( 51510 hom. )

Consequence

MAP1LC3B2
NM_001085481.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0610

Variant links:

Genes affected

MAP1LC3B2 (HGNC:34390): (microtubule associated protein 1 light chain 3 beta 2) Predicted to enable microtubule binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in autophagy of mitochondrion; cellular response to nitrogen starvation; and macroautophagy. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

MAP1LC3B2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-116576326-G-GA is Benign according to our data. Variant chr12-116576326-G-GA is described in ClinVar as [Benign]. Clinvar id is 2688190.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP1LC3B2	NM_001085481.3 linkuse as main transcript	c.*12dup		3_prime_UTR_variant	2/2	ENST00000556529.4	NP_001078950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP1LC3B2	ENST00000556529.4 linkuse as main transcript	c.*12dup		3_prime_UTR_variant	2/2	3	NM_001085481.3	ENSP00000450524	P1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37519

AN:

151182

Hom.:

5034

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.270

GnomAD3 exomes

AF:

0.257

AC:

58091

AN:

225700

Hom.:

9383

AF XY:

0.266

AC XY:

32595

AN XY:

122478

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.140

Gnomad ASJ exome

AF:

0.320

Gnomad EAS exome

AF:

0.491

Gnomad SAS exome

AF:

0.281

Gnomad FIN exome

AF:

0.276

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.261

AC:

378584

AN:

1449102

Hom.:

51510

Cov.:

AF XY:

0.265

AC XY:

190658

AN XY:

720608

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.337

Gnomad4 EAS exome

AF:

0.473

Gnomad4 SAS exome

AF:

0.302

Gnomad4 FIN exome

AF:

0.283

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.277

GnomAD4 genome

AF:

0.248

AC:

37531

AN:

151300

Hom.:

5036

Cov.:

AF XY:

0.250

AC XY:

18485

AN XY:

73904

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.495

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.266

Hom.:

1073

Bravo

AF:

0.238

Asia WGS

AF:

0.337

AC:

1171

AN:

3478

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 38% of patients studied by a panel of primary immunodeficiencies. Number of patients: 36. 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