chr14-96286247-G-A

Position:

• chr14-96286247-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_018036.7(ATG2B):​c.6007-262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,086 control chromosomes in the GnomAD database, including 3,777 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.21 (3777 hom., cov: 33)
• Consequence: ATG2B NM_018036.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.606

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 14-96286247-G-A is Benign according to our data. Variant chr14-96286247-G-A is described in ClinVar as [Benign]. Clinvar id is 1280979.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG2B	NM_018036.7	c.6007-262C>T		intron_variant		ENST00000359933.6	NP_060506.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG2B	ENST00000359933.6	c.6007-262C>T		intron_variant		5	NM_018036.7	ENSP00000353010	P1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31345 AN: 151968 Hom.: 3771 Cov.: 33

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.206 AC: 31363 AN: 152086 Hom.: 3777 Cov.: 33 AF XY: 0.207 AC XY: 15380 AN XY: 74348

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.224

Alfa AF: 0.241 Hom.: 2289

Bravo AF: 0.200

Asia WGS AF: 0.224 AC: 778 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	-0.86
CADD	Benign	0.87
DANN	Benign	0.72

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

Other links and lift over

dbSNP: rs17093991; hg19: chr14-96752584;