Variant 12-116575925-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001085481.3(MAP1LC3B2):c.-18G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 1,613,678 control chromosomes in the GnomAD database, including 373,536 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.62 ( 30499 hom., cov: 33)

Exomes 𝑓: 0.68 ( 343037 hom. )

Consequence

MAP1LC3B2
NM_001085481.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.642

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 12-116575925-G-C is Benign according to our data. Variant chr12-116575925-G-C is described in ClinVar as [Benign]. Clinvar id is 2688029.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 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.-18G>C		5_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.-18G>C		5_prime_UTR_variant	2/2	3	NM_001085481.3	ENSP00000450524	P1

Frequencies

GnomAD3 genomes

AF:

0.624

AC:

94720

AN:

151876

Hom.:

30502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.734

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.621

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.547

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.624

GnomAD3 exomes

AF:

0.595

AC:

149167

AN:

250672

Hom.:

47415

AF XY:

0.605

AC XY:

82032

AN XY:

135684

show subpopulations

Gnomad AFR exome

AF:

0.574

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.622

Gnomad EAS exome

AF:

0.279

Gnomad SAS exome

AF:

0.561

Gnomad FIN exome

AF:

0.646

Gnomad NFE exome

AF:

0.711

Gnomad OTH exome

AF:

0.637

GnomAD4 exome

AF:

0.678

AC:

990438

AN:

1461682

Hom.:

343037

Cov.:

AF XY:

0.675

AC XY:

490588

AN XY:

727154

show subpopulations

Gnomad4 AFR exome

AF:

0.573

Gnomad4 AMR exome

AF:

0.392

Gnomad4 ASJ exome

AF:

0.626

Gnomad4 EAS exome

AF:

0.300

Gnomad4 SAS exome

AF:

0.561

Gnomad4 FIN exome

AF:

0.651

Gnomad4 NFE exome

AF:

0.719

Gnomad4 OTH exome

AF:

0.651

GnomAD4 genome

AF:

0.623

AC:

94751

AN:

151996

Hom.:

30499

Cov.:

AF XY:

0.614

AC XY:

45616

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.579

Gnomad4 AMR

AF:

0.499

Gnomad4 ASJ

AF:

0.621

Gnomad4 EAS

AF:

0.286

Gnomad4 SAS

AF:

0.546

Gnomad4 FIN

AF:

0.649

Gnomad4 NFE

AF:

0.704

Gnomad4 OTH

AF:

0.624

Alfa

AF:

0.593

Hom.:

3430

Bravo

AF:

0.609

Asia WGS

AF:

0.444

AC:

1547

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 67% of patients studied by a panel of primary immunodeficiencies. Number of patients: 64. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.54

DANN

Benign

0.73

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