rs11760487
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Variant summary
Our verdict is Benign. Variant got -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
NM_001317056.2 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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: 17001AN: 151858Hom.: 1149 Cov.: 32
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GnomAD4 exome AF: 0.144 AC: 209109AN: 1449936Hom.: 16146 AF XY: 0.147 AC XY: 105732AN XY: 720160
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GnomAD4 genome ? AF: 0.112 AC: 17000AN: 151976Hom.: 1147 Cov.: 32 AF XY: 0.109 AC XY: 8109AN XY: 74304
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at