3-49718331-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198722.3(AMIGO3):c.1135G>A(p.Glu379Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMIGO3 | NM_198722.3 | c.1135G>A | p.Glu379Lys | missense_variant | Exon 1 of 1 | ENST00000320431.8 | NP_942015.1 | |
RNF123 | NM_022064.5 | c.3500+1854C>T | intron_variant | Intron 35 of 38 | ENST00000327697.11 | NP_071347.2 | ||
RNF123 | NR_135218.2 | n.3826+1854C>T | intron_variant | Intron 35 of 38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMIGO3 | ENST00000320431.8 | c.1135G>A | p.Glu379Lys | missense_variant | Exon 1 of 1 | 6 | NM_198722.3 | ENSP00000323096.7 | ||
RNF123 | ENST00000327697.11 | c.3500+1854C>T | intron_variant | Intron 35 of 38 | 1 | NM_022064.5 | ENSP00000328287.6 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000682 AC: 17AN: 249436Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135220
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461038Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 726864
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1135G>A (p.E379K) alteration is located in exon 1 (coding exon 1) of the AMIGO3 gene. This alteration results from a G to A substitution at nucleotide position 1135, causing the glutamic acid (E) at amino acid position 379 to be replaced by a lysine (K). 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