Genetic Variant ATG9B:c.821+61C>T (chr7-151022984-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.331

Publications

3 publications found

Variant links:

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]

ATG9B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATG9B	NM_001317056.2 link	c.821+61C>T		intron_variant	Intron 4 of 13	ENST00000639579.2	NP_001303985.1	Q674R7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG9B	ENST00000639579.2 link	c.821+61C>T		intron_variant	Intron 4 of 13	1	NM_001317056.2	ENSP00000491504.1		Q674R7-1
ATG9B	ENST00000605952.5 link	n.821+61C>T		intron_variant	Intron 4 of 16	1		ENSP00000475737.2		Q674R7-1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17001

AN:

151858

Hom.:

1149

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.0579

AC:

1921

AN:

33176

American (AMR)

AF:

0.0782

AC:

3465

AN:

44292

Ashkenazi Jewish (ASJ)

AF:

0.0958

AC:

2472

AN:

25816

East Asian (EAS)

AF:

0.0189

AC:

746

AN:

39522

South Asian (SAS)

AF:

0.217

AC:

18621

AN:

85646

European-Finnish (FIN)

AF:

0.101

AC:

5384

AN:

53216

Middle Eastern (MID)

AF:

0.188

AC:

1055

AN:

5598

European-Non Finnish (NFE)

AF:

0.152

AC:

167329

AN:

1102794

Other (OTH)

AF:

0.136

AC:

8116

AN:

59876

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

9561

19123

28684

38246

47807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5936

11872

17808

23744

29680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.112

AC:

17000

AN:

151976

Hom.:

1147

Cov.:

AF XY:

0.109

AC XY:

8109

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.0607

AC:

2514

AN:

41426

American (AMR)

AF:

0.0884

AC:

1351

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0899

AC:

312

AN:

3470

East Asian (EAS)

AF:

0.0135

AC:

AN:

5178

South Asian (SAS)

AF:

0.220

AC:

1055

AN:

4806

European-Finnish (FIN)

AF:

0.0948

AC:

1001

AN:

10560

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10215

AN:

67942

Other (OTH)

AF:

0.113

AC:

238

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

757

1513

2270

3026

3783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.126

Hom.:

542

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

(source)

DANN

Benign

0.80

PhyloP100

-0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over