chr11-63719787-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001265589.2(RTN3):āc.1285A>Gā(p.Lys429Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001265589.2 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 |
---|---|---|---|---|---|---|---|
RTN3 | NM_001265589.2 | c.1285A>G | p.Lys429Glu | missense_variant | 3/9 | ENST00000377819.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTN3 | ENST00000377819.10 | c.1285A>G | p.Lys429Glu | missense_variant | 3/9 | 1 | NM_001265589.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251354Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135838
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727228
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.1228A>G (p.K410E) alteration is located in exon 2 (coding exon 2) of the RTN3 gene. This alteration results from a A to G substitution at nucleotide position 1228, causing the lysine (K) at amino acid position 410 to be replaced by a glutamic acid (E). 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