7-69599651-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000403018.3(AUTS2):c.-3A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 1,297,190 control chromosomes in the GnomAD database, including 5,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.13 ( 1768 hom., cov: 32)
Exomes 𝑓: 0.079 ( 4036 hom. )
Consequence
AUTS2
ENST00000403018.3 5_prime_UTR
ENST00000403018.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.04
Genes affected
AUTS2 (HGNC:14262): (activator of transcription and developmental regulator AUTS2) This gene has been implicated in neurodevelopment and as a candidate gene for numerous neurological disorders, including autism spectrum disorders, intellectual disability, and developmental delay. Mutations in this gene have also been associated with non-neurological disorders, such as acute lymphoblastic leukemia, aging of the skin, early-onset androgenetic alopecia, and certain cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 7-69599651-A-G is Benign according to our data. Variant chr7-69599651-A-G is described in ClinVar as [Benign]. Clinvar id is 1178068.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.-3A>G | 5_prime_UTR_variant | 1/19 | ENST00000342771.10 | NP_056385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.-3A>G | 5_prime_UTR_variant | 1/19 | 1 | NM_015570.4 | ENSP00000344087 | P4 | ||
AUTS2 | ENST00000403018.3 | c.-3A>G | 5_prime_UTR_variant | 1/5 | 1 | ENSP00000385572 | ||||
AUTS2 | ENST00000406775.6 | c.-3A>G | 5_prime_UTR_variant | 1/18 | 1 | ENSP00000385263 | ||||
AUTS2 | ENST00000644939.1 | c.-3A>G | 5_prime_UTR_variant | 1/19 | ENSP00000496726 | A1 |
Frequencies
GnomAD3 genomes AF: 0.126 AC: 19102AN: 151634Hom.: 1760 Cov.: 32
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GnomAD3 exomes AF: 0.0568 AC: 497AN: 8750Hom.: 13 AF XY: 0.0576 AC XY: 263AN XY: 4564
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GnomAD4 exome AF: 0.0791 AC: 90660AN: 1145448Hom.: 4036 Cov.: 32 AF XY: 0.0790 AC XY: 43457AN XY: 550410
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GnomAD4 genome AF: 0.126 AC: 19136AN: 151742Hom.: 1768 Cov.: 32 AF XY: 0.124 AC XY: 9223AN XY: 74176
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2018 | - - |
Computational scores
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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