rs281875210
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PS1_ModeratePP3_Moderate
The NM_080669.6(SLC46A1):c.466G>T(p.Asp156Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D156H) has been classified as Uncertain significance.
Frequency
Consequence
NM_080669.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC46A1 | NM_080669.6 | c.466G>T | p.Asp156Tyr | missense_variant | 2/5 | ENST00000612814.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC46A1 | ENST00000612814.5 | c.466G>T | p.Asp156Tyr | missense_variant | 2/5 | 2 | NM_080669.6 | P1 | |
ENST00000580714.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1440194Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 714894
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at