Variant chr12-116575951-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001085481.3(MAP1LC3B2):c.9G>A(p.Ser3Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,614,158 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0095 ( 10 hom., cov: 32)

Exomes 𝑓: 0.013 ( 165 hom. )

Consequence

MAP1LC3B2
NM_001085481.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.202

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 12-116575951-G-A is Benign according to our data. Variant chr12-116575951-G-A is described in ClinVar as [Benign]. Clinvar id is 2643372.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.202 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0135 (19724/1461892) while in subpopulation MID AF= 0.0187 (108/5768). AF 95% confidence interval is 0.0159. There are 165 homozygotes in gnomad4_exome. There are 9594 alleles in male gnomad4_exome subpopulation. Median coverage is 39. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP1LC3B2	NM_001085481.3 linkuse as main transcript	c.9G>A	p.Ser3Ser	synonymous_variant	2/2	ENST00000556529.4	NP_001078950.1	A6NCE7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP1LC3B2	ENST00000556529.4 linkuse as main transcript	c.9G>A	p.Ser3Ser	synonymous_variant	2/2	3	NM_001085481.3	ENSP00000450524.1		A6NCE7

Frequencies

GnomAD3 genomes

AF:

0.00947

AC:

1441

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00270

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0103

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0153

Gnomad OTH

AF:

0.0192

GnomAD3 exomes

AF:

0.00944

AC:

2373

AN:

251430

Hom.:

AF XY:

0.00970

AC XY:

1318

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00766

Gnomad ASJ exome

AF:

0.0123

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00500

Gnomad FIN exome

AF:

0.00240

Gnomad NFE exome

AF:

0.0146

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.0135

AC:

19724

AN:

1461892

Hom.:

165

Cov.:

AF XY:

0.0132

AC XY:

9594

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.00227

Gnomad4 AMR exome

AF:

0.00816

Gnomad4 ASJ exome

AF:

0.0125

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00516

Gnomad4 FIN exome

AF:

0.00298

Gnomad4 NFE exome

AF:

0.0156

Gnomad4 OTH exome

AF:

0.0149

GnomAD4 genome

AF:

0.00946

AC:

1440

AN:

152266

Hom.:

Cov.:

AF XY:

0.00901

AC XY:

671

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00270

Gnomad4 AMR

AF:

0.0103

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.0153

Gnomad4 OTH

AF:

0.0190

Alfa

AF:

0.00954

Hom.:

Bravo

AF:

0.0101

Asia WGS

AF:

0.00202

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

Jul 01, 2024

MAP1LC3B2: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.2

DANN

Benign

0.74

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