chr12-47078174-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370299.1(AMIGO2):c.829G>A(p.Asp277Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,614,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370299.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMIGO2 | NM_001370299.1 | c.829G>A | p.Asp277Asn | missense_variant | 3/3 | ENST00000550413.2 | |
AMIGO2 | NM_001143668.1 | c.829G>A | p.Asp277Asn | missense_variant | 3/3 | ||
AMIGO2 | NM_181847.4 | c.829G>A | p.Asp277Asn | missense_variant | 2/2 | ||
AMIGO2 | XM_047428785.1 | c.829G>A | p.Asp277Asn | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMIGO2 | ENST00000550413.2 | c.829G>A | p.Asp277Asn | missense_variant | 3/3 | 1 | NM_001370299.1 | P1 | |
AMIGO2 | ENST00000266581.4 | c.829G>A | p.Asp277Asn | missense_variant | 2/2 | 1 | P1 | ||
AMIGO2 | ENST00000429635.1 | c.829G>A | p.Asp277Asn | missense_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251462Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135906
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.000154 AC XY: 112AN XY: 727248
GnomAD4 genome AF: 0.000125 AC: 19AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.829G>A (p.D277N) alteration is located in exon 2 (coding exon 1) of the AMIGO2 gene. This alteration results from a G to A substitution at nucleotide position 829, causing the aspartic acid (D) at amino acid position 277 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at