7-69599757-C-CCGG
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting
The NM_015570(AUTS2):c.114_116dup(p.Gly38dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000264 in 151516 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Consequence
AUTS2
NM_015570 inframe_insertion
NM_015570 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.147
Links
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.0000264 (4/151516) while in subpopulation AFR AF= 0.0000968 (4/41304). AF 95% confidence interval is 0.0000326. There are 0 homozygotes in gnomad. There are 3 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.114_116dup | p.Gly38dup | inframe_insertion | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.114_116dup | p.Gly38dup | inframe_insertion | 1/19 | 1 | NM_015570.4 | P4 | |
AUTS2 | ENST00000403018.3 | c.114_116dup | p.Gly38dup | inframe_insertion | 1/5 | 1 | |||
AUTS2 | ENST00000406775.6 | c.114_116dup | p.Gly38dup | inframe_insertion | 1/18 | 1 | |||
AUTS2 | ENST00000644939.1 | c.114_116dup | p.Gly38dup | inframe_insertion | 1/19 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151516Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000189 AC: 23AN: 1219330Hom.: 0 AF XY: 0.0000168 AC XY: 10AN XY: 595024
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autism spectrum disorder due to AUTS2 deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PerkinElmer Genomics | Mar 19, 2021 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In-frame insertion of 1 amino acid in a repetitive region with no known function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at