1-109508086-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020703.4(AMIGO1):c.827G>A(p.Arg276His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,614,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020703.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMIGO1 | NM_020703.4 | c.827G>A | p.Arg276His | missense_variant | 2/2 | ENST00000369864.5 | |
AMIGO1 | XM_011541812.3 | c.827G>A | p.Arg276His | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMIGO1 | ENST00000369864.5 | c.827G>A | p.Arg276His | missense_variant | 2/2 | 1 | NM_020703.4 | P1 | |
AMIGO1 | ENST00000369862.1 | c.827G>A | p.Arg276His | missense_variant | 2/2 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251456Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135906
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727232
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.827G>A (p.R276H) alteration is located in exon 2 (coding exon 1) of the AMIGO1 gene. This alteration results from a G to A substitution at nucleotide position 827, causing the arginine (R) at amino acid position 276 to be replaced by a histidine (H). 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