5-176629600-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003085.5(SNCB):c.55G>A(p.Ala19Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,568 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461394Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727008
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
Lewy body dementia Uncertain:1
The observed missense variant c.55G>A(p.Ala19Thr) in SNCB gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.55G>A variant is reported with 0 frequency in gnomAD Exomes. The amino acid Alanine at position 19 is changed to a Threonine changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence (Polyphen-Probably damaging, SIFT-Damaging and Mutation Taster-Disease causing) predict a damaging effect on protein structure and function for this variant. The reference amino acid p.Ala19Thr in SNCB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at