rs6568431

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000636437.1(ATG5):​c.457+61041T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,130 control chromosomes in the GnomAD database, including 28,291 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 0.61 ( 28291 hom., cov: 33)

Consequence

ATG5
ENST00000636437.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.759
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATG5ENST00000636437.1 linkuse as main transcriptc.457+61041T>G intron_variant 5 ENSP00000490376
ATG5ENST00000636335.1 linkuse as main transcriptc.457+61041T>G intron_variant, NMD_transcript_variant 5 ENSP00000490221

Frequencies

GnomAD3 genomes
AF:
0.608
AC:
92415
AN:
152012
Hom.:
28261
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.591
Gnomad AMI
AF:
0.614
Gnomad AMR
AF:
0.653
Gnomad ASJ
AF:
0.592
Gnomad EAS
AF:
0.645
Gnomad SAS
AF:
0.624
Gnomad FIN
AF:
0.538
Gnomad MID
AF:
0.644
Gnomad NFE
AF:
0.616
Gnomad OTH
AF:
0.618
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.608
AC:
92509
AN:
152130
Hom.:
28291
Cov.:
33
AF XY:
0.606
AC XY:
45039
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.591
Gnomad4 AMR
AF:
0.653
Gnomad4 ASJ
AF:
0.592
Gnomad4 EAS
AF:
0.646
Gnomad4 SAS
AF:
0.627
Gnomad4 FIN
AF:
0.538
Gnomad4 NFE
AF:
0.616
Gnomad4 OTH
AF:
0.618
Alfa
AF:
0.620
Hom.:
39548
Bravo
AF:
0.619
Asia WGS
AF:
0.637
AC:
2218
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.5
DANN
Benign
0.68

Splicing

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.

Other links and lift over

dbSNP: rs6568431; hg19: chr6-106588806; COSMIC: COSV55571756; API