rs77474263
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018242.3(SLC47A1):c.373C>T(p.Leu125Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00518 in 1,614,144 control chromosomes in the GnomAD database, including 523 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 0.0082 ( 59 hom., cov: 31)
Exomes 𝑓: 0.0049 ( 464 hom. )
Consequence
SLC47A1
NM_018242.3 missense
NM_018242.3 missense
Scores
1
9
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.71
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 (MetaRNN=0.0039165616).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0663 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC47A1 | NM_018242.3 | c.373C>T | p.Leu125Phe | missense_variant | 4/17 | ENST00000270570.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC47A1 | ENST00000270570.8 | c.373C>T | p.Leu125Phe | missense_variant | 4/17 | 1 | NM_018242.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00818 AC: 1245AN: 152194Hom.: 58 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0209 AC: 5259AN: 251360Hom.: 389 AF XY: 0.0157 AC XY: 2136AN XY: 135874
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GnomAD4 exome AF: 0.00487 AC: 7119AN: 1461832Hom.: 464 Cov.: 30 AF XY: 0.00417 AC XY: 3030AN XY: 727224
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GnomAD4 genome ? AF: 0.00820 AC: 1249AN: 152312Hom.: 59 Cov.: 31 AF XY: 0.00990 AC XY: 737AN XY: 74462
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.;D
REVEL
Uncertain
Sift
Uncertain
D;D;.;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
D;D;.;D
Vest4
MPC
0.72
ClinPred
T
GERP RS
Varity_R
gMVP
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