Variant chr16-87398847-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_022818.5(MAP1LC3B):c.73G>C(p.Glu25Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,614,034 control chromosomes in the GnomAD database, including 125 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0071 ( 7 hom., cov: 33)

Exomes 𝑓: 0.010 ( 118 hom. )

Consequence

MAP1LC3B
NM_022818.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.91

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0095620155).

BP6

Variant 16-87398847-G-C is Benign according to our data. Variant chr16-87398847-G-C is described in ClinVar as [Benign]. Clinvar id is 781343.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP1LC3B	NM_022818.5 linkuse as main transcript	c.73G>C	p.Glu25Gln	missense_variant	2/4	ENST00000268607.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP1LC3B	ENST00000268607.10 linkuse as main transcript	c.73G>C	p.Glu25Gln	missense_variant	2/4	1	NM_022818.5	P1
	ENST00000569147.1 linkuse as main transcript	n.275+1174C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00708

AC:

1077

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00234

Gnomad AMI

AF:

0.0811

Gnomad AMR

AF:

0.00465

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00349

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0114

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00605

AC:

1521

AN:

251484

Hom.:

AF XY:

0.00617

AC XY:

838

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00228

Gnomad ASJ exome

AF:

0.00278

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000425

Gnomad FIN exome

AF:

0.00416

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.00521

GnomAD4 exome

AF:

0.0105

AC:

15277

AN:

1461738

Hom.:

118

Cov.:

AF XY:

0.0102

AC XY:

7427

AN XY:

727164

show subpopulations

Gnomad4 AFR exome

AF:

0.00173

Gnomad4 AMR exome

AF:

0.00230

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000499

Gnomad4 FIN exome

AF:

0.00350

Gnomad4 NFE exome

AF:

0.0129

Gnomad4 OTH exome

AF:

0.00874

GnomAD4 genome

AF:

0.00707

AC:

1077

AN:

152296

Hom.:

Cov.:

AF XY:

0.00661

AC XY:

492

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00233

Gnomad4 AMR

AF:

0.00464

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00349

Gnomad4 NFE

AF:

0.0114

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00963

Hom.:

Bravo

AF:

0.00732

TwinsUK

AF:

0.0140

AC:

ALSPAC

AF:

0.0127

AC:

ESP6500AA

AF:

0.00205

AC:

ESP6500EA

AF:

0.0128

AC:

110

ExAC

AF:

0.00637

AC:

774

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0100

EpiControl

AF:

0.0116

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

Invitae

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.42

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.12

T;.

Eigen

Uncertain

0.27

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.92

D;D

MetaRNN

Benign

0.0096

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.4

L;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.78

PROVEAN

Benign

-1.8

N;N

REVEL

Benign

0.061

Sift

Benign

0.17

T;T

Sift4G

Benign

0.32

T;T

Polyphen

0.55

P;.

Vest4

0.48

MVP

0.70

MPC

0.81

ClinPred

0.043

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.63

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