1-109507531-T-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020703.4(AMIGO1):c.1382A>T(p.Asn461Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00024 in 1,614,012 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMIGO1 | NM_020703.4 | c.1382A>T | p.Asn461Ile | missense_variant | 2/2 | ENST00000369864.5 | |
AMIGO1 | XM_011541812.3 | c.1382A>T | p.Asn461Ile | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMIGO1 | ENST00000369864.5 | c.1382A>T | p.Asn461Ile | missense_variant | 2/2 | 1 | NM_020703.4 | P1 | |
AMIGO1 | ENST00000369862.1 | c.1382A>T | p.Asn461Ile | missense_variant | 2/2 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251418Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135886
GnomAD4 exome AF: 0.000250 AC: 365AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.000238 AC XY: 173AN XY: 727232
GnomAD4 genome AF: 0.000151 AC: 23AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1382A>T (p.N461I) alteration is located in exon 2 (coding exon 1) of the AMIGO1 gene. This alteration results from a A to T substitution at nucleotide position 1382, causing the asparagine (N) at amino acid position 461 to be replaced by an isoleucine (I). 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