rs34904447
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032808.7(LINGO1):c.885C>T(p.Ser295=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_032808.7 synonymous
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 |
---|---|---|---|---|---|---|---|
LINGO1 | NM_032808.7 | c.885C>T | p.Ser295= | synonymous_variant | 2/2 | ENST00000355300.7 | |
LOC105370906 | XR_001751806.2 | n.689-15263G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINGO1 | ENST00000355300.7 | c.885C>T | p.Ser295= | synonymous_variant | 2/2 | 1 | NM_032808.7 | A1 | |
LINGO1 | ENST00000561030.5 | c.867C>T | p.Ser289= | synonymous_variant | 4/4 | 1 | P4 | ||
LINGO1 | ENST00000557798.1 | c.900C>T | p.Ser300= | synonymous_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249278Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135224
GnomAD4 exome AF: 0.000187 AC: 273AN: 1461704Hom.: 0 Cov.: 56 AF XY: 0.000188 AC XY: 137AN XY: 727136
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at