7-151023815-A-G

Variant names:

• chr7-151023815-A-G
• rs13307588
• NM_001317056.2:c.550+59T>C

Variant summary

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

The NM_001317056.2(ATG9B):​c.550+59T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 1,611,684 control chromosomes in the GnomAD database, including 716,718 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 0.96 (69574 hom., cov: 32)
  • Exomes 𝑓: 0.94 (647144 hom.)
• Consequence: ATG9B NM_001317056.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 9 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001317056.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG9B	NM_001317056.2	MANE Select	c.550+59T>C		intron	N/A	NP_001303985.1	Q674R7-1
	ATG9B	NR_073169.1		n.233+59T>C		intron	N/A
	ATG9B	NR_133652.1		n.626+59T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG9B	ENST00000639579.2	TSL:1 MANE Select	c.550+59T>C		intron	N/A	ENSP00000491504.1	Q674R7-1
	ATG9B	ENST00000605952.5	TSL:1	n.550+59T>C		intron	N/A	ENSP00000475737.2	Q674R7-1
	ATG9B	ENST00000617967.4	TSL:1	n.199+59T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.956 AC: 145353 AN: 152112 Hom.: 69514 Cov.: 32

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.951

GnomAD4 exome AF: 0.941 AC: 1373994 AN: 1459454 Hom.: 647144 Cov.: 51 AF XY: 0.942 AC XY: 684026 AN XY: 725940

African (AFR) AF: 0.990 AC: 33110 AN: 33454

American (AMR) AF: 0.969 AC: 43222 AN: 44604

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 25242 AN: 25934

East Asian (EAS) AF: 1.00 AC: 39663 AN: 39672

South Asian (SAS) AF: 0.980 AC: 84257 AN: 85986

European-Finnish (FIN) AF: 0.945 AC: 49986 AN: 52912

Middle Eastern (MID) AF: 0.970 AC: 5585 AN: 5756

European-Non Finnish (NFE) AF: 0.932 AC: 1035695 AN: 1110820

Other (OTH) AF: 0.949 AC: 57234 AN: 60316

GnomAD4 genome AF: 0.956 AC: 145472 AN: 152230 Hom.: 69574 Cov.: 32 AF XY: 0.956 AC XY: 71120 AN XY: 74418

African (AFR) AF: 0.988 AC: 41046 AN: 41528

American (AMR) AF: 0.951 AC: 14543 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3382 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5172

South Asian (SAS) AF: 0.979 AC: 4724 AN: 4826

European-Finnish (FIN) AF: 0.938 AC: 9951 AN: 10612

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.934 AC: 63540 AN: 68010

Other (OTH) AF: 0.951 AC: 2005 AN: 2108

Alfa AF: 0.950 Hom.: 24056

Bravo AF: 0.958

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.32
PhyloP100		-2.4
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: rs13307588; hg19: chr7-150720902;