rs3743162
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004213.5(SLC28A1):c.-16-7C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004213.5 splice_region, 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC28A1 | NM_004213.5 | c.-16-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000394573.6 | NP_004204.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.-16-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004213.5 | ENSP00000378074 | P1 | |||
SLC28A1 | ENST00000286749.3 | c.-16-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000286749 | P1 | ||||
SLC28A1 | ENST00000338602.6 | c.-16-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000341629 | |||||
SLC28A1 | ENST00000538177.5 | c.-16-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | ENSP00000443752 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at