rs1058600

chr5-115831016-C-T

Variant summary

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

The NM_004707.4(ATG12):c.*788G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,034 control chromosomes in the GnomAD database, including 12,590 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 0.36 (12590 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATG12 NM_004707.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

Genes affected

ATG12 (HGNC:588): (autophagy related 12) Autophagy is a process of bulk protein degradation in which cytoplasmic components, including organelles, are enclosed in double-membrane structures called autophagosomes and delivered to lysosomes or vacuoles for degradation. ATG12 is the human homolog of a yeast protein involved in autophagy (Mizushima et al., 1998 [PubMed 9852036]).[supplied by OMIM, Mar 2008]

LOC124901049 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG12	NM_004707.4	c.*788G>A		3_prime_UTR_variant	4/4	ENST00000509910.2
LOC124901049	XR_007058908.1	n.85-1235C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG12	ENST00000509910.2	c.*788G>A		3_prime_UTR_variant	4/4	1	NM_004707.4	P1
ATG12	ENST00000500945.2	c.*849G>A		3_prime_UTR_variant	3/3	1
ATG12	ENST00000505252.1	n.2599G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54967 AN: 151914 Hom.: 12539 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.355

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.362 AC: 55088 AN: 152034 Hom.: 12590 Cov.: 32 AF XY: 0.361 AC XY: 26824 AN XY: 74322

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.354

Alfa AF: 0.252 Hom.: 8977

Bravo AF: 0.396

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.18
Dann	Benign	0.32

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: rs1058600; hg19: chr5-115166713;