7-69599781-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate
The NM_015570(AUTS2):c.128C>T(p.Thr43Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T43T) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
AUTS2
NM_015570 missense
NM_015570 missense
Scores
2
1
10
Clinical Significance
Conservation
PhyloP100: 1.12
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.17338657).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.128C>T | p.Thr43Ile | missense_variant | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.128C>T | p.Thr43Ile | missense_variant | 1/19 | 1 | NM_015570.4 | P4 | |
AUTS2 | ENST00000406775.6 | c.128C>T | p.Thr43Ile | missense_variant | 1/18 | 1 | |||
AUTS2 | ENST00000403018.3 | c.128C>T | p.Thr43Ile | missense_variant | 1/5 | 1 | |||
AUTS2 | ENST00000644939.1 | c.128C>T | p.Thr43Ile | missense_variant | 1/19 | A1 |
Frequencies
GnomAD3 genomesCov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000545 AC: 3AN: 550482Hom.: 0 AF XY: 0.00000668 AC XY: 2AN XY: 299284
GnomAD4 exome
AF:
AC:
3
AN:
550482
Hom.:
AF XY:
AC XY:
2
AN XY:
299284
Gnomad4 AFR exome
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Gnomad4 AMR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 NFE exome
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Gnomad4 OTH exome
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Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autism spectrum disorder due to AUTS2 deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PerkinElmer Genomics | Apr 19, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Pathogenic
D
Polyphen
0.078
.;B;B;.
Vest4
0.095, 0.081, 0.097
MutPred
Loss of phosphorylation at T43 (P = 0.0064);Loss of phosphorylation at T43 (P = 0.0064);Loss of phosphorylation at T43 (P = 0.0064);Loss of phosphorylation at T43 (P = 0.0064);
MVP
0.093
MPC
2.6
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out SpliceAI and Pangolin per-transcript scores at