6-106300336-A-G

Position:

• chr6-106300336-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004849.4(ATG5):​c.237-7230T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 152,206 control chromosomes in the GnomAD database, including 734 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 0.075 (734 hom., cov: 32)
• Consequence: ATG5 NM_004849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

Genes affected

ATG5 (HGNC:589): (autophagy related 5) The protein encoded by this gene, in combination with autophagy protein 12, functions as an E1-like activating enzyme in a ubiquitin-like conjugating system. The encoded protein is involved in several cellular processes, including autophagic vesicle formation, mitochondrial quality control after oxidative damage, negative regulation of the innate antiviral immune response, lymphocyte development and proliferation, MHC II antigen presentation, adipocyte differentiation, and apoptosis. Several transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

ATG5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG5	NM_004849.4	c.237-7230T>C		intron_variant		ENST00000369076.8	NP_004840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG5	ENST00000369076.8	c.237-7230T>C		intron_variant		1	NM_004849.4	ENSP00000358072.3

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11409 AN: 152088 Hom.: 727 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0750 AC: 11423 AN: 152206 Hom.: 734 Cov.: 32 AF XY: 0.0768 AC XY: 5714 AN XY: 74420

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0505

Gnomad4 NFE AF: 0.0737

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0752 Hom.: 247

Bravo AF: 0.0921

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.80

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: rs10485352; hg19: chr6-106748211;