7-69599697-G-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015570.4(AUTS2):c.44G>T(p.Arg15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AUTS2
NM_015570.4 missense
NM_015570.4 missense
Scores
4
2
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.13
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19225648).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.44G>T | p.Arg15Leu | missense_variant | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.44G>T | p.Arg15Leu | missense_variant | 1/19 | 1 | NM_015570.4 | P4 | |
AUTS2 | ENST00000406775.6 | c.44G>T | p.Arg15Leu | missense_variant | 1/18 | 1 | |||
AUTS2 | ENST00000403018.3 | c.44G>T | p.Arg15Leu | missense_variant | 1/5 | 1 | |||
AUTS2 | ENST00000644939.1 | c.44G>T | p.Arg15Leu | missense_variant | 1/19 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1173954Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 567692
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1173954
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
567692
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;L;L
MutationTaster
Benign
N;N;N
PrimateAI
Pathogenic
D
PROVEAN
Benign
.;N;N;D
REVEL
Benign
Sift
Pathogenic
.;D;D;D
Sift4G
Uncertain
.;D;D;D
Polyphen
0.0030
.;B;B;.
Vest4
0.13, 0.14, 0.14
MutPred
Gain of glycosylation at K13 (P = 0.1127);Gain of glycosylation at K13 (P = 0.1127);Gain of glycosylation at K13 (P = 0.1127);Gain of glycosylation at K13 (P = 0.1127);
MVP
0.11
MPC
2.4
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.