3-49718561-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_198722.3(AMIGO3):c.905C>A(p.Thr302Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,770 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
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.905C>A | p.Thr302Asn | missense_variant | Exon 1 of 1 | ENST00000320431.8 | NP_942015.1 | |
RNF123 | NM_022064.5 | c.3501-1950G>T | intron_variant | Intron 35 of 38 | ENST00000327697.11 | NP_071347.2 | ||
RNF123 | NR_135218.2 | n.3827-1950G>T | intron_variant | Intron 35 of 38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMIGO3 | ENST00000320431.8 | c.905C>A | p.Thr302Asn | missense_variant | Exon 1 of 1 | 6 | NM_198722.3 | ENSP00000323096.7 | ||
RNF123 | ENST00000327697.11 | c.3501-1950G>T | intron_variant | Intron 35 of 38 | 1 | NM_022064.5 | ENSP00000328287.6 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460770Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726720
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.905C>A (p.T302N) alteration is located in exon 1 (coding exon 1) of the AMIGO3 gene. This alteration results from a C to A substitution at nucleotide position 905, causing the threonine (T) at amino acid position 302 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
Publications
No publications associated with this variant yet.