3-49718307-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_198722.3(AMIGO3):āc.1159A>Gā(p.Thr387Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000093 in 1,613,066 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198722.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMIGO3 | NM_198722.3 | c.1159A>G | p.Thr387Ala | missense_variant | Exon 1 of 1 | ENST00000320431.8 | NP_942015.1 | |
RNF123 | NM_022064.5 | c.3500+1830T>C | intron_variant | Intron 35 of 38 | ENST00000327697.11 | NP_071347.2 | ||
RNF123 | NR_135218.2 | n.3826+1830T>C | intron_variant | Intron 35 of 38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMIGO3 | ENST00000320431.8 | c.1159A>G | p.Thr387Ala | missense_variant | Exon 1 of 1 | 6 | NM_198722.3 | ENSP00000323096.7 | ||
RNF123 | ENST00000327697.11 | c.3500+1830T>C | intron_variant | Intron 35 of 38 | 1 | NM_022064.5 | ENSP00000328287.6 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000724 AC: 18AN: 248748Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 134948
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1460904Hom.: 0 Cov.: 31 AF XY: 0.0000977 AC XY: 71AN XY: 726810
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1159A>G (p.T387A) alteration is located in exon 1 (coding exon 1) of the AMIGO3 gene. This alteration results from a A to G substitution at nucleotide position 1159, causing the threonine (T) at amino acid position 387 to be replaced by an alanine (A). 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