rs2286064

Variant names:

• chrX-112778421-G-C
• rs2286064
• NM_001113490.2:c.*146C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-112778421-G-C
• chrX-112778421-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001113490.2(AMOT):​c.*146C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 481,997 control chromosomes in the GnomAD database, including 1,711 homozygotes. There are 14,130 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 0.079 (307 hom., 2733 hem., cov: 23)
  • Exomes 𝑓: 0.10 (1404 hom. 11397 hem.)
• Consequence: AMOT NM_001113490.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.79
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMOT	NM_001113490.2	c.*146C>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000371959.9	NP_001106962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMOT	ENST00000371959.9	c.*146C>G		3_prime_UTR_variant	Exon 14 of 14	1	NM_001113490.2	ENSP00000361027.3
AMOT	ENST00000304758.5	c.*146C>G		3_prime_UTR_variant	Exon 12 of 12	1		ENSP00000305557.1
AMOT	ENST00000371962.5	c.*146C>G		downstream_gene_variant		1		ENSP00000361030.1

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 8793 AN: 111544 Hom.: 305 Cov.: 23

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0711

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0858

GnomAD4 exome AF: 0.101 AC: 37379 AN: 370407 Hom.: 1404 Cov.: 5 AF XY: 0.102 AC XY: 11397 AN XY: 111389

African (AFR) AF: 0.0191 AC: 217 AN: 11362

American (AMR) AF: 0.125 AC: 2771 AN: 22201

Ashkenazi Jewish (ASJ) AF: 0.0681 AC: 686 AN: 10070

East Asian (EAS) AF: 0.108 AC: 2757 AN: 25642

South Asian (SAS) AF: 0.0774 AC: 1852 AN: 23940

European-Finnish (FIN) AF: 0.146 AC: 3563 AN: 24401

Middle Eastern (MID) AF: 0.0822 AC: 202 AN: 2458

European-Non Finnish (NFE) AF: 0.102 AC: 23423 AN: 229488

Other (OTH) AF: 0.0915 AC: 1908 AN: 20845

GnomAD4 genome AF: 0.0789 AC: 8802 AN: 111590 Hom.: 307 Cov.: 23 AF XY: 0.0809 AC XY: 2733 AN XY: 33796

African (AFR) AF: 0.0208 AC: 639 AN: 30681

American (AMR) AF: 0.0910 AC: 960 AN: 10544

Ashkenazi Jewish (ASJ) AF: 0.0642 AC: 170 AN: 2648

East Asian (EAS) AF: 0.105 AC: 371 AN: 3536

South Asian (SAS) AF: 0.0738 AC: 196 AN: 2655

European-Finnish (FIN) AF: 0.145 AC: 867 AN: 5988

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.0991 AC: 5265 AN: 53123

Other (OTH) AF: 0.0920 AC: 140 AN: 1522

Alfa AF: 0.0969 Hom.: 552

Bravo AF: 0.0746

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.6
DANN	Benign	0.75
PhyloP100		2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2286064; hg19: chrX-112021649;