Variant X-112779389-GCTGGAGCAGCAGCAGCAGCAACAGCAA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_001113490.2(AMOT):c.2738_2764delTTGCTGTTGCTGCTGCTGCTGCTCCAG(p.Val913_Pro921del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 1,080,297 control chromosomes in the GnomAD database, including 200 homozygotes. There are 6,795 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 12 hom., 451 hem., cov: 22)

Exomes 𝑓: 0.022 ( 188 hom. 6344 hem. )

Consequence

AMOT
NM_001113490.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.83

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 -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001113490.2

BP6

Variant X-112779389-GCTGGAGCAGCAGCAGCAGCAACAGCAA-G is Benign according to our data. Variant chrX-112779389-GCTGGAGCAGCAGCAGCAGCAACAGCAA-G is described in ClinVar as [Benign]. Clinvar id is 771229.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.015 (1675/112027) while in subpopulation NFE AF= 0.021 (1116/53097). AF 95% confidence interval is 0.02. There are 12 homozygotes in gnomad4. There are 451 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMOT	NM_001113490.2 link	c.2738_2764delTTGCTGTTGCTGCTGCTGCTGCTCCAG	p.Val913_Pro921del	disruptive_inframe_deletion	13/14	ENST00000371959.9	NP_001106962.1	Q4VCS5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AMOT	ENST00000371959.9 link	c.2738_2764delTTGCTGTTGCTGCTGCTGCTGCTCCAG	p.Val913_Pro921del	disruptive_inframe_deletion	13/14	1	NM_001113490.2	ENSP00000361027.3	Q4VCS5-1
AMOT	ENST00000371962.5 link	c.2042_2068delTTGCTGTTGCTGCTGCTGCTGCTCCAG	p.Val681_Pro689del	disruptive_inframe_deletion	10/11	1		ENSP00000361030.1	E7ERM3
AMOT	ENST00000304758.5 link	c.1511_1537delTTGCTGTTGCTGCTGCTGCTGCTCCAG	p.Val504_Pro512del	disruptive_inframe_deletion	11/12	1		ENSP00000305557.1	Q4VCS5-2

Frequencies

GnomAD3 genomes

AF:

0.0150

AC:

1675

AN:

111977

Hom.:

Cov.:

AF XY:

0.0132

AC XY:

451

AN XY:

34179

show subpopulations

Gnomad AFR

AF:

0.00873

Gnomad AMI

AF:

0.0247

Gnomad AMR

AF:

0.0185

Gnomad ASJ

AF:

0.0143

Gnomad EAS

AF:

0.000278

Gnomad SAS

AF:

0.00189

Gnomad FIN

AF:

0.00114

Gnomad MID

AF:

0.0169

Gnomad NFE

AF:

0.0210

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.0152

AC:

1783

AN:

117459

Hom.:

AF XY:

0.0132

AC XY:

524

AN XY:

39847

show subpopulations

Gnomad AFR exome

AF:

0.00961

Gnomad AMR exome

AF:

0.0118

Gnomad ASJ exome

AF:

0.0190

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00297

Gnomad FIN exome

AF:

0.00410

Gnomad NFE exome

AF:

0.0264

Gnomad OTH exome

AF:

0.0159

GnomAD4 exome

AF:

0.0223

AC:

21603

AN:

968270

Hom.:

188

AF XY:

0.0221

AC XY:

6344

AN XY:

286870

show subpopulations

Gnomad4 AFR exome

AF:

0.0112

Gnomad4 AMR exome

AF:

0.0133

Gnomad4 ASJ exome

AF:

0.0181

Gnomad4 EAS exome

AF:

0.0000371

Gnomad4 SAS exome

AF:

0.00360

Gnomad4 FIN exome

AF:

0.00424

Gnomad4 NFE exome

AF:

0.0262

Gnomad4 OTH exome

AF:

0.0200

GnomAD4 genome

AF:

0.0150

AC:

1675

AN:

112027

Hom.:

Cov.:

AF XY:

0.0132

AC XY:

451

AN XY:

34239

show subpopulations

Gnomad4 AFR

AF:

0.00871

Gnomad4 AMR

AF:

0.0184

Gnomad4 ASJ

AF:

0.0143

Gnomad4 EAS

AF:

0.000278

Gnomad4 SAS

AF:

0.00189

Gnomad4 FIN

AF:

0.00114

Gnomad4 NFE

AF:

0.0210

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.0190

Hom.:

126

Bravo

AF:

0.0171

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 09, 2019

- -

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