Genetic Variant MAP1LC3B:c.41-2182C>T (chr16-87396633-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022818.5(MAP1LC3B):c.41-2182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 151,940 control chromosomes in the GnomAD database, including 46,426 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.78 ( 46425 hom., cov: 30)

Exomes 𝑓: 0.67 ( 1 hom. )

Consequence

MAP1LC3B
NM_022818.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.479

Publications

14 publications found

Variant links:

Genes affected

MAP1LC3B (HGNC:13352): (microtubule associated protein 1 light chain 3 beta) The product of this gene is a subunit of neuronal microtubule-associated MAP1A and MAP1B proteins, which are involved in microtubule assembly and important for neurogenesis. Studies on the rat homolog implicate a role for this gene in autophagy, a process that involves the bulk degradation of cytoplasmic component. [provided by RefSeq, Jul 2008]

MAP1LC3B links:

ENSG00000261592 (HGNC:):

ENSG00000261592 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022818.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP1LC3B	NM_022818.5	MANE Select	c.41-2182C>T		intron	N/A	NP_073729.1	Q9GZQ8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAP1LC3B	ENST00000268607.10	TSL:1 MANE Select	c.41-2182C>T	intron	N/A	ENSP00000268607.5	Q9GZQ8
MAP1LC3B	ENST00000564844.1	TSL:1	n.*686-2182C>T	intron	N/A	ENSP00000454293.1	H3BM99
MAP1LC3B	ENST00000570189.5	TSL:1	n.41-2182C>T	intron	N/A	ENSP00000457141.1	H3BTE7

Frequencies

GnomAD3 genomes

AF:

0.778

AC:

118168

AN:

151818

Hom.:

46406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.733

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.709

Gnomad ASJ

AF:

0.728

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.848

Gnomad FIN

AF:

0.839

Gnomad MID

AF:

0.666

Gnomad NFE

AF:

0.826

Gnomad OTH

AF:

0.764

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.775

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.778

AC:

118232

AN:

151934

Hom.:

46425

Cov.:

AF XY:

0.773

AC XY:

57401

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.732

AC:

30322

AN:

41396

American (AMR)

AF:

0.708

AC:

10806

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.728

AC:

2525

AN:

3470

East Asian (EAS)

AF:

0.562

AC:

2889

AN:

5144

South Asian (SAS)

AF:

0.848

AC:

4073

AN:

4804

European-Finnish (FIN)

AF:

0.839

AC:

8867

AN:

10568

Middle Eastern (MID)

AF:

0.658

AC:

192

AN:

292

European-Non Finnish (NFE)

AF:

0.826

AC:

56177

AN:

67984

Other (OTH)

AF:

0.763

AC:

1606

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1263

2525

3788

5050

6313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.805

Hom.:

192163

Bravo

AF:

0.760

Asia WGS

AF:

0.715

AC:

2489

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.73

(source)

DANN

Benign

0.52

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over