3-49718748-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198722.3(AMIGO3):c.718A>G(p.Ser240Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMIGO3 | NM_198722.3 | c.718A>G | p.Ser240Gly | missense_variant | 1/1 | ENST00000320431.8 | |
RNF123 | NM_022064.5 | c.3501-1763T>C | intron_variant | ENST00000327697.11 | |||
RNF123 | NR_135218.2 | n.3827-1763T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMIGO3 | ENST00000320431.8 | c.718A>G | p.Ser240Gly | missense_variant | 1/1 | NM_198722.3 | P1 | ||
RNF123 | ENST00000327697.11 | c.3501-1763T>C | intron_variant | 1 | NM_022064.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460802Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726750
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.718A>G (p.S240G) 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 718, causing the serine (S) at amino acid position 240 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