rs807185

chrX-108097488-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_052936.5(ATG4A):c.10+5652A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.73 (21159 hom., 23436 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ATG4A NM_052936.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

ATG4A (HGNC:16489): (autophagy related 4A 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. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 21162 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG4A	NM_052936.5	c.10+5652A>T		intron_variant		ENST00000372232.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG4A	ENST00000372232.8	c.10+5652A>T		intron_variant		1	NM_052936.5	P1

Frequencies

GnomAD3 genomes AF: 0.728 AC: 80070 AN: 110022 Hom.: 21162 Cov.: 22 AF XY: 0.725 AC XY: 23382 AN XY: 32272

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.746

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.706

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.728 AC: 80116 AN: 110076 Hom.: 21159 Cov.: 22 AF XY: 0.725 AC XY: 23436 AN XY: 32336

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.706

Alfa AF: 0.707 Hom.: 5738

Bravo AF: 0.733

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.76

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: rs807185; hg19: chrX-107340718;