5-102459786-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173488.5(SLCO6A1):c.900-9T>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000257 in 1,554,962 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_173488.5 splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
SLCO6A1 | NM_173488.5 | c.900-9T>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000506729.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO6A1 | ENST00000506729.6 | c.900-9T>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_173488.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151436Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1403526Hom.: 0 Cov.: 31 AF XY: 0.00000143 AC XY: 1AN XY: 698344
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151436Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 73886
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at