7-69599664-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015570(AUTS2):c.11C>T(p.Pro4Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00289 in 152036 control chromosomes in the gnomAD Genomes database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0029 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 1 hom. )
Consequence
AUTS2
NM_015570 missense
NM_015570 missense
Scores
1
4
7
Clinical Significance
Conservation
PhyloP100: 5.82
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0038175583).
BP6
?
Variant 7:69599664-C>T is Benign according to our data. Variant chr7-69599664-C-T is described in ClinVar as [Benign]. Clinvar id is 975656. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-69599664-C-T is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.00289 (440/152036) while in subpopulation NFE AF= 0.00512 (348/67974). AF 95% confidence interval is 0.00468. There are 2 homozygotes in gnomad. There are 177 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 440 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.11C>T | p.Pro4Leu | missense_variant | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.11C>T | p.Pro4Leu | missense_variant | 1/19 | 1 | NM_015570.4 | P4 | |
AUTS2 | ENST00000406775.6 | c.11C>T | p.Pro4Leu | missense_variant | 1/18 | 1 | |||
AUTS2 | ENST00000403018.3 | c.11C>T | p.Pro4Leu | missense_variant | 1/5 | 1 | |||
AUTS2 | ENST00000644939.1 | c.11C>T | p.Pro4Leu | missense_variant | 1/19 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00289 AC: 440AN: 152036Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00341 AC: 38AN: 11154Hom.: 1 AF XY: 0.00368 AC XY: 22AN XY: 5974
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GnomAD4 exome AF: 0.00483 AC: 5563AN: 1152222Hom.: 22 AF XY: 0.00471 AC XY: 2610AN XY: 554422
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg | Mar 21, 2023 | This variant has been identified by standard clinical testing. - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | Criteria applied: PP2, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 31, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 28, 2018 | - - |
Intellectual disability Benign:1
Likely benign, no assertion criteria provided | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
Polyphen
1.0
.;D;D;.
Vest4
0.38, 0.37, 0.47
MVP
0.47
MPC
2.6
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at