12-47077521-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001370299.1(AMIGO2):c.1482G>A(p.Glu494Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00371 in 1,614,150 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 76 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 81 hom. )
Consequence
AMIGO2
NM_001370299.1 synonymous
NM_001370299.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.46
Genes affected
AMIGO2 (HGNC:24073): (adhesion molecule with Ig like domain 2) Predicted to be involved in several processes, including heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; homophilic cell adhesion via plasma membrane adhesion molecules; and negative regulation of programmed cell death. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in nucleus and plasma membrane. Predicted to be integral component of membrane. Biomarker of gastric adenocarcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 12-47077521-C-T is Benign according to our data. Variant chr12-47077521-C-T is described in ClinVar as [Benign]. Clinvar id is 779523.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.46 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMIGO2 | NM_001370299.1 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 3 of 3 | ENST00000550413.2 | NP_001357228.1 | |
AMIGO2 | NM_001143668.1 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 3 of 3 | NP_001137140.1 | ||
AMIGO2 | NM_181847.4 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 2 of 2 | NP_862830.1 | ||
AMIGO2 | XM_047428785.1 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 2 of 2 | XP_047284741.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMIGO2 | ENST00000550413.2 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 3 of 3 | 1 | NM_001370299.1 | ENSP00000449034.1 | ||
AMIGO2 | ENST00000266581.4 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000266581.4 | |||
AMIGO2 | ENST00000429635.1 | c.1482G>A | p.Glu494Glu | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000406020.1 |
Frequencies
GnomAD3 genomes AF: 0.0173 AC: 2632AN: 152170Hom.: 76 Cov.: 33
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GnomAD3 exomes AF: 0.00472 AC: 1187AN: 251344Hom.: 19 AF XY: 0.00361 AC XY: 490AN XY: 135850
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GnomAD4 exome AF: 0.00230 AC: 3357AN: 1461862Hom.: 81 Cov.: 30 AF XY: 0.00205 AC XY: 1489AN XY: 727226
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GnomAD4 genome AF: 0.0173 AC: 2637AN: 152288Hom.: 76 Cov.: 33 AF XY: 0.0169 AC XY: 1262AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at