3-49718412-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_198722.3(AMIGO3):āc.1054T>Gā(p.Cys352Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,612,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMIGO3 | NM_198722.3 | c.1054T>G | p.Cys352Gly | missense_variant | Exon 1 of 1 | ENST00000320431.8 | NP_942015.1 | |
RNF123 | NM_022064.5 | c.3500+1935A>C | intron_variant | Intron 35 of 38 | ENST00000327697.11 | NP_071347.2 | ||
RNF123 | NR_135218.2 | n.3826+1935A>C | intron_variant | Intron 35 of 38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMIGO3 | ENST00000320431.8 | c.1054T>G | p.Cys352Gly | missense_variant | Exon 1 of 1 | 6 | NM_198722.3 | ENSP00000323096.7 | ||
RNF123 | ENST00000327697.11 | c.3500+1935A>C | intron_variant | Intron 35 of 38 | 1 | NM_022064.5 | ENSP00000328287.6 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249888Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135472
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460692Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726680
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1054T>G (p.C352G) alteration is located in exon 1 (coding exon 1) of the AMIGO3 gene. This alteration results from a T to G substitution at nucleotide position 1054, causing the cysteine (C) at amino acid position 352 to be replaced by a glycine (G). 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