rs763438860
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_152424.4(AMER1):c.1034C>T(p.Ala345Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000909 in 1,210,671 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 24)
Exomes 𝑓: 0.0000082 ( 0 hom. 5 hem. )
Consequence
AMER1
NM_152424.4 missense
NM_152424.4 missense
Scores
1
1
14
Clinical Significance
Conservation
PhyloP100: 5.98
Genes affected
AMER1 (HGNC:26837): (APC membrane recruitment protein 1) The protein encoded by this gene upregulates trancriptional activation by the Wilms tumor protein and interacts with many other proteins, including CTNNB1, APC, AXIN1, and AXIN2. Defects in this gene are a cause of osteopathia striata with cranial sclerosis (OSCS). [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.19301823).
BP6
?
Variant X-64192253-G-A is Benign according to our data. Variant chrX-64192253-G-A is described in ClinVar as [Benign]. Clinvar id is 208535.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAdExome4 at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMER1 | NM_152424.4 | c.1034C>T | p.Ala345Val | missense_variant | 2/2 | ENST00000374869.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMER1 | ENST00000374869.8 | c.1034C>T | p.Ala345Val | missense_variant | 2/2 | 5 | NM_152424.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112397Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34547
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GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183414Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67848
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GnomAD4 exome AF: 0.00000820 AC: 9AN: 1098220Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 5AN XY: 363576
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GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112451Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34611
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spinocerebellar ataxia, X-linked Uncertain:1
Uncertain significance, no assertion criteria provided | case-control | Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 22, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;M
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
P;P
Vest4
MVP
MPC
0.085
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at