chr1-62811233-G-A

Variant names:

• chr1-62811233-G-A
• rs6683832
• NM_032852.4:c.161-5342G>A

Variant summary

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

The NM_032852.4(ATG4C):​c.161-5342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,080 control chromosomes in the GnomAD database, including 31,088 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 0.64 (31088 hom., cov: 34)
• Consequence: ATG4C NM_032852.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 4 publications found

Genes affected

ATG4C (HGNC:16040): (autophagy related 4C cysteine peptidase) Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding the same protein, have been characterized. [provided by RefSeq, Jul 2008]

ENSG00000306496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032852.4. 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
	ATG4C	NM_032852.4	MANE Select	c.161-5342G>A		intron	N/A	NP_116241.2
	ATG4C	NM_178221.3		c.161-5342G>A		intron	N/A	NP_835739.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG4C	ENST00000317868.9	TSL:1 MANE Select	c.161-5342G>A		intron	N/A	ENSP00000322159.4
	ATG4C	ENST00000371120.7	TSL:1	c.161-5342G>A		intron	N/A	ENSP00000360161.3
	ATG4C	ENST00000371118.1	TSL:5	c.161-5342G>A		intron	N/A	ENSP00000360159.1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96695 AN: 151962 Hom.: 31051 Cov.: 34

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.636 AC: 96784 AN: 152080 Hom.: 31088 Cov.: 34 AF XY: 0.639 AC XY: 47512 AN XY: 74340

African (AFR) AF: 0.732 AC: 30412 AN: 41528

American (AMR) AF: 0.707 AC: 10794 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1922 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3560 AN: 5180

South Asian (SAS) AF: 0.627 AC: 3030 AN: 4830

European-Finnish (FIN) AF: 0.533 AC: 5636 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39381 AN: 67926

Other (OTH) AF: 0.639 AC: 1349 AN: 2110

Alfa AF: 0.614 Hom.: 3736

Bravo AF: 0.654

Asia WGS AF: 0.637 AC: 2213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.64
PhyloP100		0.35
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: rs6683832; hg19: chr1-63276904;