Variant 14-96290636-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018036.7(ATG2B):c.5702-46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00854 in 1,606,812 control chromosomes in the GnomAD database, including 737 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 369 hom., cov: 33)

Exomes 𝑓: 0.0054 ( 368 hom. )

Consequence

ATG2B
NM_018036.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.671

Variant links:

Genes affected

ATG2B (HGNC:20187): (autophagy related 2B) This gene encodes a protein required for autophagy. The encoded protein is involved in autophagosome formation. A germline duplication of a region that includes this gene is associated with predisposition to myeloid malignancies. [provided by RefSeq, Jul 2016]

ATG2B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 14-96290636-T-C is Benign according to our data. Variant chr14-96290636-T-C is described in ClinVar as [Benign]. Clinvar id is 1260376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG2B	NM_018036.7 linkuse as main transcript	c.5702-46A>G		intron_variant		ENST00000359933.6	NP_060506.6

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
ATG2B	ENST00000359933.6 linkuse as main transcript	c.5702-46A>G	intron_variant	5	NM_018036.7	ENSP00000353010	P1
ATG2B	ENST00000261834.9 linkuse as main transcript	n.1688-46A>G	intron_variant, non_coding_transcript_variant	2
ATG2B	ENST00000553643.1 linkuse as main transcript	n.462-46A>G	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.0383

AC:

5824

AN:

152138

Hom.:

368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.0446

Gnomad NFE

AF:

0.00196

Gnomad OTH

AF:

0.0316

GnomAD3 exomes

AF:

0.0118

AC:

2902

AN:

246592

Hom.:

177

AF XY:

0.00902

AC XY:

1202

AN XY:

133300

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.0121

Gnomad ASJ exome

AF:

0.00277

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000335

Gnomad FIN exome

AF:

0.000188

Gnomad NFE exome

AF:

0.00229

Gnomad OTH exome

AF:

0.0117

GnomAD4 exome

AF:

0.00542

AC:

7883

AN:

1454556

Hom.:

368

Cov.:

AF XY:

0.00485

AC XY:

3502

AN XY:

722626

show subpopulations

Gnomad4 AFR exome

AF:

0.135

Gnomad4 AMR exome

AF:

0.0130

Gnomad4 ASJ exome

AF:

0.00178

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000350

Gnomad4 FIN exome

AF:

0.000132

Gnomad4 NFE exome

AF:

0.00172

Gnomad4 OTH exome

AF:

0.0122

GnomAD4 genome

AF:

0.0384

AC:

5840

AN:

152256

Hom.:

369

Cov.:

AF XY:

0.0363

AC XY:

2700

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.0210

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00196

Gnomad4 OTH

AF:

0.0313

Alfa

AF:

0.0226

Hom.:

Bravo

AF:

0.0440

Asia WGS

AF:

0.00866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

DANN

Benign

0.55

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