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GeneBe

7-69599693-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PM2_SupportingBP4

The NM_015570.4(AUTS2):c.40C>T(p.Arg14Trp) 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_015570.4 missense

Scores

3
4
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.649

Links

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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=0.38335857).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AUTS2NM_015570.4 linkuse as main transcriptc.40C>T p.Arg14Trp missense_variant 1/19 ENST00000342771.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AUTS2ENST00000342771.10 linkuse as main transcriptc.40C>T p.Arg14Trp missense_variant 1/191 NM_015570.4 P4Q8WXX7-1
AUTS2ENST00000406775.6 linkuse as main transcriptc.40C>T p.Arg14Trp missense_variant 1/181 Q8WXX7-2
AUTS2ENST00000403018.3 linkuse as main transcriptc.40C>T p.Arg14Trp missense_variant 1/51 Q8WXX7-3
AUTS2ENST00000644939.1 linkuse as main transcriptc.40C>T p.Arg14Trp missense_variant 1/19 A1

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxMay 11, 2023Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.93
BayesDel_addAF
Benign
-0.044
T
BayesDel_noAF
Benign
-0.30
Cadd
Pathogenic
29
Dann
Uncertain
1.0
Eigen
Uncertain
0.28
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Benign
0.56
D
LIST_S2
Uncertain
0.90
D;D;D;D
M_CAP
Pathogenic
0.90
D
MetaRNN
Benign
0.38
T;T;T;T
MetaSVM
Benign
-0.80
T
MutationTaster
Benign
0.90
N;N;N
PrimateAI
Pathogenic
0.98
D
Polyphen
0.99, 0.98
.;D;D;.
Vest4
0.32, 0.33, 0.50
MutPred
0.27
Loss of methylation at K12 (P = 0.0542);Loss of methylation at K12 (P = 0.0542);Loss of methylation at K12 (P = 0.0542);Loss of methylation at K12 (P = 0.0542);
MVP
0.33
MPC
2.6
ClinPred
0.94
D
GERP RS
3.6
Varity_R
0.23
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-69064679; COSMIC: COSV61423980; COSMIC: COSV61423980; API