Variant X-112780929-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001113490.2(AMOT):c.2430C>A(p.Ile810Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 1,209,693 control chromosomes in the GnomAD database, including 3,496 homozygotes. There are 31,266 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.097 ( 509 hom., 3290 hem., cov: 23)

Exomes 𝑓: 0.073 ( 2987 hom. 27976 hem. )

Consequence

AMOT
NM_001113490.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

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]

AMOT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP7

Synonymous conserved (PhyloP=1.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMOT	NM_001113490.2 link	c.2430C>A	p.Ile810Ile	synonymous_variant	12/14	ENST00000371959.9	NP_001106962.1	Q4VCS5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AMOT	ENST00000371959.9 link	c.2430C>A	p.Ile810Ile	synonymous_variant	12/14	1	NM_001113490.2	ENSP00000361027.3	Q4VCS5-1
AMOT	ENST00000371962.5 link	c.1734C>A	p.Ile578Ile	synonymous_variant	9/11	1		ENSP00000361030.1	E7ERM3
AMOT	ENST00000304758.5 link	c.1203C>A	p.Ile401Ile	synonymous_variant	10/12	1		ENSP00000305557.1	Q4VCS5-2
AMOT	ENST00000371958.1 link	c.1734C>A	p.Ile578Ile	synonymous_variant	9/9	5		ENSP00000361026.1	A6NP16

Frequencies

GnomAD3 genomes

AF:

0.0975

AC:

10872

AN:

111514

Hom.:

508

Cov.:

AF XY:

0.0975

AC XY:

3287

AN XY:

33716

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.0659

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.0764

Gnomad MID

AF:

0.0756

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0980

GnomAD3 exomes

AF:

0.121

AC:

22124

AN:

183368

Hom.:

1345

AF XY:

0.117

AC XY:

7938

AN XY:

67810

show subpopulations

Gnomad AFR exome

AF:

0.144

Gnomad AMR exome

AF:

0.259

Gnomad ASJ exome

AF:

0.0622

Gnomad EAS exome

AF:

0.177

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.0856

Gnomad NFE exome

AF:

0.0508

Gnomad OTH exome

AF:

0.0974

GnomAD4 exome

AF:

0.0725

AC:

79638

AN:

1098131

Hom.:

2987

Cov.:

AF XY:

0.0770

AC XY:

27976

AN XY:

363497

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.0632

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.215

Gnomad4 FIN exome

AF:

0.0788

Gnomad4 NFE exome

AF:

0.0493

Gnomad4 OTH exome

AF:

0.0818

GnomAD4 genome

AF:

0.0975

AC:

10873

AN:

111562

Hom.:

509

Cov.:

AF XY:

0.0974

AC XY:

3290

AN XY:

33774

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.0659

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.195

Gnomad4 FIN

AF:

0.0764

Gnomad4 NFE

AF:

0.0496

Gnomad4 OTH

AF:

0.0961

Alfa

AF:

0.0618

Hom.:

2211

Bravo

AF:

0.114

EpiCase

AF:

0.0470

EpiControl

AF:

0.0460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

5.6

DANN

Benign

0.78

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over