7-69599669-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PM2_SupportingBP4
The NM_015570(AUTS2):c.16C>T(p.Arg6Trp) 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 (★).
Frequency
Genomes: not found (cov: 32)
Consequence
AUTS2
NM_015570 missense
NM_015570 missense
Scores
2
2
9
Clinical Significance
Conservation
PhyloP100: 1.40
Links
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance.
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.39441597).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.16C>T | p.Arg6Trp | missense_variant | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.16C>T | p.Arg6Trp | missense_variant | 1/19 | 1 | NM_015570.4 | P4 | |
AUTS2 | ENST00000406775.6 | c.16C>T | p.Arg6Trp | missense_variant | 1/18 | 1 | |||
AUTS2 | ENST00000403018.3 | c.16C>T | p.Arg6Trp | missense_variant | 1/5 | 1 | |||
AUTS2 | ENST00000644939.1 | c.16C>T | p.Arg6Trp | missense_variant | 1/19 | A1 |
Frequencies
GnomAD3 genomesCov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000311 AC: 1AN: 321472Hom.: 0 AF XY: 0.00000584 AC XY: 1AN XY: 171202
GnomAD4 exome
AF:
AC:
1
AN:
321472
Hom.:
AF XY:
AC XY:
1
AN XY:
171202
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.16C>T (p.R6W) alteration is located in exon 1 (coding exon 1) of the AUTS2 gene. This alteration results from a C to T substitution at nucleotide position 16, causing the arginine (R) at amino acid position 6 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Pathogenic
D
Polyphen
0.89
.;P;P;.
Vest4
0.25, 0.21, 0.28
MutPred
Loss of methylation at R6 (P = 0.0069);Loss of methylation at R6 (P = 0.0069);Loss of methylation at R6 (P = 0.0069);Loss of methylation at R6 (P = 0.0069);
MVP
0.23
MPC
2.6
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at