7-69599740-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015570.4(AUTS2):c.87G>T(p.Gly29Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000222 in 1,349,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
AUTS2
NM_015570.4 synonymous
NM_015570.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.540
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 was made for transcript
Our verdict: Benign. The variant received -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 7-69599740-G-T is Benign according to our data. Variant chr7-69599740-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2892806.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.54 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0000132 (2/151856) while in subpopulation SAS AF = 0.000414 (2/4830). AF 95% confidence interval is 0.0000729. There are 0 homozygotes in GnomAd4. There are 2 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
BS2
High AC in GnomAdExome4 at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.87G>T | p.Gly29Gly | synonymous_variant | Exon 1 of 19 | ENST00000342771.10 | NP_056385.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151748Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
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2
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32
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GnomAD2 exomes AF: 0.000130 AC: 2AN: 15426 AF XY: 0.000240 show subpopulations
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GnomAD4 exome AF: 0.0000234 AC: 28AN: 1197808Hom.: 0 Cov.: 32 AF XY: 0.0000327 AC XY: 19AN XY: 581822 show subpopulations
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10188
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15966
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27216
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26
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43050
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38056
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1
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987574
Gnomad4 Remaining exome
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1
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48650
Heterozygous variant carriers
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151856Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74246 show subpopulations
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 20, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
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