X-112778421-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001113490.2(AMOT):​c.*146C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001113490.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMOT	NM_001113490.2	MANE Select	c.*146C>A		3_prime_UTR	Exon 14 of 14	NP_001106962.1	Q4VCS5-1
	AMOT	NM_001386998.1		c.*146C>A		3_prime_UTR	Exon 15 of 15	NP_001373927.1	Q4VCS5-1
	AMOT	NM_001386999.1		c.*146C>A		3_prime_UTR	Exon 14 of 14	NP_001373928.1	Q4VCS5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMOT	ENST00000371959.9	TSL:1 MANE Select	c.*146C>A		3_prime_UTR	Exon 14 of 14	ENSP00000361027.3	Q4VCS5-1
	AMOT	ENST00000304758.5	TSL:1	c.*146C>A		3_prime_UTR	Exon 12 of 12	ENSP00000305557.1	Q4VCS5-2
	AMOT	ENST00000371962.5	TSL:1	c.*146C>A		downstream_gene	N/A	ENSP00000361030.1	E7ERM3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 370643 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 111437

African (AFR) AF: 0.00 AC: 0 AN: 11364

American (AMR) AF: 0.00 AC: 0 AN: 22219

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10075

East Asian (EAS) AF: 0.00 AC: 0 AN: 25651

South Asian (SAS) AF: 0.00 AC: 0 AN: 23943

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2462

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 229650

Other (OTH) AF: 0.00 AC: 0 AN: 20857

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.4
DANN	Benign	0.72
PhyloP100		2.8

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;