rs3792109

chr2-233275771-G-Achr2-233275771-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_030803.7(ATG16L1):c.954+993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 518,942 control chromosomes in the GnomAD database, including 59,027 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 0.42 (14453 hom., cov: 32)
  • Exomes 𝑓: 0.48 (44574 hom.)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

ATG16L1 (HGNC:21498): (autophagy related 16 like 1) The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]

SCARNA5 (HGNC:32561): (small Cajal body-specific RNA 5)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG16L1	NM_030803.7	c.954+993G>A		intron_variant		ENST00000392017.9
SCARNA5	NR_003008.2	n.46G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG16L1	ENST00000392017.9	c.954+993G>A		intron_variant		1	NM_030803.7	P3
SCARNA5	ENST00000516201.1	n.45G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63736 AN: 151908 Hom.: 14460 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.433

GnomAD3 exomes AF: 0.450 AC: 104492 AN: 232064 Hom.: 25491 AF XY: 0.467 AC XY: 59805 AN XY: 128008

Gnomad AFR exome AF: 0.256

Gnomad AMR exome AF: 0.236

Gnomad ASJ exome AF: 0.611

Gnomad EAS exome AF: 0.333

Gnomad SAS exome AF: 0.520

Gnomad FIN exome AF: 0.448

Gnomad NFE exome AF: 0.526

Gnomad OTH exome AF: 0.476

GnomAD4 exome AF: 0.480 AC: 176026 AN: 366916 Hom.: 44574 Cov.: 0 AF XY: 0.492 AC XY: 103557 AN XY: 210390

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.607

Gnomad4 EAS exome AF: 0.326

Gnomad4 SAS exome AF: 0.525

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.527

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.419 AC: 63725 AN: 152026 Hom.: 14453 Cov.: 32 AF XY: 0.415 AC XY: 30832 AN XY: 74320

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.428

Alfa AF: 0.506 Hom.: 31183

Bravo AF: 0.403

Asia WGS AF: 0.356 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	9.0
Dann	Benign	0.88
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.3

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: rs3792109; hg19: chr2-234184417; COSMIC: COSV61463985; COSMIC: COSV61463985;