chr11-63719646-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.1144A>Gā(p.Ser382Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.1144A>G | p.Ser382Gly | missense_variant | 3/9 | ENST00000377819.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTN3 | ENST00000377819.10 | c.1144A>G | p.Ser382Gly | missense_variant | 3/9 | 1 | NM_001265589.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000840 AC: 21AN: 250098Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135466
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461614Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727130
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74510
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at