rs11760487

Positions:

• chr7-151022984-G-A

Variant summary

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

The NM_001317056.2(ATG9B):​c.821+61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,601,912 control chromosomes in the GnomAD database, including 17,293 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 0.11 (1147 hom., cov: 32)
  • Exomes 𝑓: 0.14 (16146 hom.)
• Consequence: ATG9B NM_001317056.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

Genes affected

ATG9B (HGNC:21899): (autophagy related 9B) This gene functions in the regulation of autophagy, a lysosomal degradation pathway. This gene also functions as an antisense transcript in the posttranscriptional regulation of the endothelial nitric oxide synthase 3 gene, which has 3' overlap with this gene on the opposite strand. Mutations in this gene and disruption of the autophagy process have been associated with multiple cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG9B	NM_001317056.2	c.821+61C>T		intron_variant		ENST00000639579.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG9B	ENST00000639579.2	c.821+61C>T		intron_variant		1	NM_001317056.2	P1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17001 AN: 151858 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.0608

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.144 AC: 209109 AN: 1449936 Hom.: 16146 AF XY: 0.147 AC XY: 105732 AN XY: 720160

Gnomad4 AFR exome AF: 0.0579

Gnomad4 AMR exome AF: 0.0782

Gnomad4 ASJ exome AF: 0.0958

Gnomad4 EAS exome AF: 0.0189

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.112 AC: 17000 AN: 151976 Hom.: 1147 Cov.: 32 AF XY: 0.109 AC XY: 8109 AN XY: 74304

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.113

Alfa AF: 0.128 Hom.: 300

Bravo AF: 0.104

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.80

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: rs11760487; hg19: chr7-150720071; COSMIC: COSV65060229; COSMIC: COSV65060229;