rs4905480

Variant names:

• chr14-96293516-A-C
• rs4905480
• NM_018036.7:c.5427-1418T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018036.7(ATG2B):​c.5427-1418T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,062 control chromosomes in the GnomAD database, including 9,876 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (9876 hom., cov: 32)
• Consequence: ATG2B NM_018036.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018036.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG2B	NM_018036.7	MANE Select	c.5427-1418T>G		intron	N/A	NP_060506.6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG2B	ENST00000359933.6	TSL:5 MANE Select	c.5427-1418T>G		intron	N/A	ENSP00000353010.4
	ATG2B	ENST00000261834.9	TSL:2	n.1413-1418T>G		intron	N/A
	ATG2B	ENST00000554151.1	TSL:3	n.101-302T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52879 AN: 151942 Hom.: 9877 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.348 AC: 52892 AN: 152062 Hom.: 9876 Cov.: 32 AF XY: 0.342 AC XY: 25409 AN XY: 74324

African (AFR) AF: 0.239 AC: 9916 AN: 41484

American (AMR) AF: 0.406 AC: 6198 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5180

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4824

European-Finnish (FIN) AF: 0.349 AC: 3680 AN: 10552

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28765 AN: 67954

Other (OTH) AF: 0.326 AC: 690 AN: 2116

Alfa AF: 0.400 Hom.: 53791

Bravo AF: 0.350

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.51
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4905480; hg19: chr14-96759853;