Variant chrX-112779450-TGGCAGCAGTGGCAGTGATGGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2

The ENST00000371959.9(AMOT):c.2683_2703del(p.Ala895_Ala901del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000116 in 1,193,612 control chromosomes in the GnomAD database, including 3 homozygotes. There are 35 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000054 ( 0 hom., 1 hem., cov: 22)

Exomes 𝑓: 0.00012 ( 3 hom. 34 hem. )

Consequence

AMOT
ENST00000371959.9 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.55

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.

BP3

Nonframeshift variant in repetitive region in ENST00000371959.9

BP6

Variant X-112779450-TGGCAGCAGTGGCAGTGATGGC-T is Benign according to our data. Variant chrX-112779450-TGGCAGCAGTGGCAGTGATGGC-T is described in ClinVar as [Likely_benign]. Clinvar id is 715548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMOT	NM_001113490.2 linkuse as main transcript	c.2683_2703del	p.Ala895_Ala901del	inframe_deletion	13/14	ENST00000371959.9	NP_001106962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMOT	ENST00000371959.9 linkuse as main transcript	c.2683_2703del	p.Ala895_Ala901del	inframe_deletion	13/14	1	NM_001113490.2	ENSP00000361027	P3	Q4VCS5-1
AMOT	ENST00000304758.5 linkuse as main transcript	c.1456_1476del	p.Ala486_Ala492del	inframe_deletion	11/12	1		ENSP00000305557	A2	Q4VCS5-2
AMOT	ENST00000371962.5 linkuse as main transcript	c.1987_2007del	p.Ala663_Ala669del	inframe_deletion	10/11	1		ENSP00000361030	A2

Frequencies

GnomAD3 genomes

AF:

0.0000538

AC:

AN:

111557

Hom.:

Cov.:

AF XY:

0.0000296

AC XY:

AN XY:

33795

show subpopulations

Gnomad AFR

AF:

0.0000978

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000952

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000561

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000152

AC:

AN:

151613

Hom.:

AF XY:

0.0000641

AC XY:

AN XY:

46789

show subpopulations

Gnomad AFR exome

AF:

0.000386

Gnomad AMR exome

AF:

0.0000819

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00119

Gnomad SAS exome

AF:

0.000121

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000255

GnomAD4 exome

AF:

0.000122

AC:

132

AN:

1082055

Hom.:

AF XY:

0.0000966

AC XY:

AN XY:

351869

show subpopulations

Gnomad4 AFR exome

AF:

0.0000767

Gnomad4 AMR exome

AF:

0.0000910

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000576

Gnomad4 SAS exome

AF:

0.0000191

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000960

Gnomad4 OTH exome

AF:

0.00222

GnomAD4 genome

AF:

0.0000538

AC:

AN:

111557

Hom.:

Cov.:

AF XY:

0.0000296

AC XY:

AN XY:

33795

show subpopulations

Gnomad4 AFR

AF:

0.0000978

Gnomad4 AMR

AF:

0.0000952

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000561

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.000159

Asia WGS

AF:

0.00199

AC:

AN:

2522

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2023	AMOT: BS2 -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over