rs2289669
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018242.3(SLC47A1):c.922-158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 596,556 control chromosomes in the GnomAD database, including 50,253 homozygotes. 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
Genomes: 𝑓 0.33 ( 10151 hom., cov: 31)
Exomes 𝑓: 0.42 ( 40102 hom. )
Consequence
SLC47A1
NM_018242.3 intron
NM_018242.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.375
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC47A1 | NM_018242.3 | c.922-158G>A | intron_variant | ENST00000270570.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC47A1 | ENST00000270570.8 | c.922-158G>A | intron_variant | 1 | NM_018242.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.328 AC: 49826AN: 151828Hom.: 10159 Cov.: 31
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GnomAD4 exome AF: 0.416 AC: 185032AN: 444610Hom.: 40102 AF XY: 0.422 AC XY: 98895AN XY: 234528
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GnomAD4 genome ? AF: 0.328 AC: 49814AN: 151946Hom.: 10151 Cov.: 31 AF XY: 0.333 AC XY: 24711AN XY: 74252
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at