Variant 14-96286218-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018036.7(ATG2B):c.6007-233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,118 control chromosomes in the GnomAD database, including 42,220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.74 ( 42220 hom., cov: 33)

Consequence

ATG2B
NM_018036.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0770

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 -14 ACMG points.

BP4

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

BP6

Variant 14-96286218-C-T is Benign according to our data. Variant chr14-96286218-C-T is described in ClinVar as [Benign]. Clinvar id is 1282005.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 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.6007-233G>A		intron_variant		ENST00000359933.6	NP_060506.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG2B	ENST00000359933.6 linkuse as main transcript	c.6007-233G>A		intron_variant		5	NM_018036.7	ENSP00000353010	P1

Frequencies

GnomAD3 genomes

AF:

0.744

AC:

113052

AN:

152000

Hom.:

42200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.792

Gnomad AMI

AF:

0.605

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.696

Gnomad EAS

AF:

0.780

Gnomad SAS

AF:

0.723

Gnomad FIN

AF:

0.704

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.723

Gnomad OTH

AF:

0.734

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.744

AC:

113114

AN:

152118

Hom.:

42220

Cov.:

AF XY:

0.745

AC XY:

55383

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.792

Gnomad4 AMR

AF:

0.747

Gnomad4 ASJ

AF:

0.696

Gnomad4 EAS

AF:

0.780

Gnomad4 SAS

AF:

0.721

Gnomad4 FIN

AF:

0.704

Gnomad4 NFE

AF:

0.723

Gnomad4 OTH

AF:

0.731

Alfa

AF:

0.733

Hom.:

15955

Bravo

AF:

0.747

Asia WGS

AF:

0.751

AC:

2614

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

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.33

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