rs138992506

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001113490.2(AMOT):​c.3095C>T​(p.Ala1032Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000335 in 1,207,493 control chromosomes in the GnomAD database, including 5 homozygotes. There are 109 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0019 ( 2 hom., 55 hem., cov: 23)
Exomes 𝑓: 0.00018 ( 3 hom. 54 hem. )

Consequence

AMOT
NM_001113490.2 missense

Scores

1
2
14

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.72
Variant links:
Genes affected
AMOT (HGNC:17810): (angiomotin) This gene belongs to the motin family of angiostatin binding proteins characterized by conserved coiled-coil domains and C-terminal PDZ binding motifs. The encoded protein is expressed predominantly in endothelial cells of capillaries as well as larger vessels of the placenta where it may mediate the inhibitory effect of angiostatin on tube formation and the migration of endothelial cells toward growth factors during the formation of new blood vessels. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.004874915).
BP6
Variant X-112779059-G-A is Benign according to our data. Variant chrX-112779059-G-A is described in ClinVar as [Benign]. Clinvar id is 781558.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AMOTNM_001113490.2 linkc.3095C>T p.Ala1032Val missense_variant Exon 13 of 14 ENST00000371959.9 NP_001106962.1 Q4VCS5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AMOTENST00000371959.9 linkc.3095C>T p.Ala1032Val missense_variant Exon 13 of 14 1 NM_001113490.2 ENSP00000361027.3 Q4VCS5-1
AMOTENST00000371962.5 linkc.2399C>T p.Ala800Val missense_variant Exon 10 of 11 1 ENSP00000361030.1 E7ERM3
AMOTENST00000304758.5 linkc.1868C>T p.Ala623Val missense_variant Exon 11 of 12 1 ENSP00000305557.1 Q4VCS5-2

Frequencies

GnomAD3 genomes
AF:
0.00186
AC:
205
AN:
110118
Hom.:
2
Cov.:
23
AF XY:
0.00169
AC XY:
55
AN XY:
32638
show subpopulations
Gnomad AFR
AF:
0.00631
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000578
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000385
Gnomad OTH
AF:
0.00273
GnomAD3 exomes
AF:
0.000495
AC:
89
AN:
179926
Hom.:
1
AF XY:
0.000304
AC XY:
20
AN XY:
65782
show subpopulations
Gnomad AFR exome
AF:
0.00579
Gnomad AMR exome
AF:
0.000477
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000183
AC:
201
AN:
1097322
Hom.:
3
Cov.:
30
AF XY:
0.000149
AC XY:
54
AN XY:
362688
show subpopulations
Gnomad4 AFR exome
AF:
0.00659
Gnomad4 AMR exome
AF:
0.000369
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000238
Gnomad4 OTH exome
AF:
0.000239
GnomAD4 genome
AF:
0.00185
AC:
204
AN:
110171
Hom.:
2
Cov.:
23
AF XY:
0.00168
AC XY:
55
AN XY:
32701
show subpopulations
Gnomad4 AFR
AF:
0.00629
Gnomad4 AMR
AF:
0.000481
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000385
Gnomad4 OTH
AF:
0.00270
Alfa
AF:
0.000267
Hom.:
7
Bravo
AF:
0.00220
ESP6500AA
AF:
0.00495
AC:
19
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000469
AC:
57

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Nov 14, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.088
BayesDel_addAF
Benign
-0.77
T
BayesDel_noAF
Benign
-0.87
CADD
Benign
18
DANN
Uncertain
0.99
DEOGEN2
Benign
0.032
T;.;T;T
FATHMM_MKL
Benign
0.67
D
LIST_S2
Benign
0.51
T;T;T;.
M_CAP
Benign
0.0069
T
MetaRNN
Benign
0.0049
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.55
N;.;.;N
PrimateAI
Benign
0.42
T
PROVEAN
Benign
-0.36
N;N;N;N
REVEL
Benign
0.027
Sift
Pathogenic
0.0
D;.;D;D
Sift4G
Uncertain
0.016
D;D;D;D
Polyphen
0.0
B;.;.;B
Vest4
0.16
MVP
0.20
MPC
1.0
ClinPred
0.083
T
GERP RS
3.3
Varity_R
0.12
gMVP
0.10

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs138992506; hg19: chrX-112022287; API