Variant rs2241880 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030803.7(ATG16L1):c.898A>G(p.Thr300Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151798 control chromosomes in the gnomAD Genomes database, including 15197 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 15197 hom., cov: 32)

Exomes 𝑓: 0.45 ( 27569 hom. )

Consequence

ATG16L1
NM_030803.7 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: -0.448

Links

ATG16L1 (HGNC:21498):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.8645105E-5).

BA1

GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG16L1	NM_030803.7 linkuse as main transcript	c.898A>G	p.Thr300Ala	missense_variant	9/18	ENST00000392017.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG16L1	ENST00000392017.9 linkuse as main transcript	c.898A>G	p.Thr300Ala	missense_variant	9/18	1	NM_030803.7	P3	Q676U5-1

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66455

AN:

151798

Hom.:

15197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.528

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.443

GnomAD3 exomes

AF:

0.453

AC:

113606

AN:

250652

Hom.:

27569

AF XY:

0.469

AC XY:

63500

AN XY:

135462

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.238

Gnomad ASJ exome

AF:

0.617

Gnomad EAS exome

AF:

0.333

Gnomad SAS exome

AF:

0.521

Gnomad FIN exome

AF:

0.449

Gnomad NFE exome

AF:

0.523

Gnomad OTH exome

AF:

0.475

GnomAD4 exome

AF:

0.502

AC:

730915

AN:

1457198

Hom.:

188220

AF XY:

0.504

AC XY:

365648

AN XY:

725132

show subpopulations

Gnomad4 AFR exome

AF:

0.320

Gnomad4 AMR exome

AF:

0.252

Gnomad4 ASJ exome

AF:

0.611

Gnomad4 EAS exome

AF:

0.278

Gnomad4 SAS exome

AF:

0.526

Gnomad4 FIN exome

AF:

0.442

Gnomad4 NFE exome

AF:

0.524

Gnomad4 OTH exome

AF:

0.489

Alfa

AF:

0.506

Hom.:

49100

Bravo

AF:

0.423

TwinsUK

AF:

0.524

AC:

1942

ALSPAC

AF:

0.520

AC:

2005

ESP6500AA

AF:

0.324

AC:

1428

ESP6500EA

AF:

0.524

AC:

4506

ExAC

AF:

0.457

AC:

55525

Asia WGS

AF:

0.359

AC:

1250

AN:

3478

EpiCase

AF:

0.531

EpiControl

AF:

0.522

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Feb 24, 2015

- -

Inflammatory bowel disease 10, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 27, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

Cadd

Benign

0.37

Dann

Benign

0.71

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.034

MetaRNN

Benign

0.000019

T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.10

N;N;N;N;N;N;N

REVEL

Benign

0.072

Sift

Benign

0.61

T;T;T;T;.;T;T

Sift4G

Benign

1.0

T;T;T;T;T;T;T

Polyphen

0.0, 0.0010

.;B;.;B;.;B;.

Vest4

0.049

MPC

0.56

ClinPred

0.017

GERP RS

-11

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.026

gMVP

0.21

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over