rs7827290
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001286646.2(SLC45A4):c.-401+17880A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,920 control chromosomes in the GnomAD database, including 6,143 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 0.27 ( 6143 hom., cov: 31)
Consequence
SLC45A4
NM_001286646.2 intron
NM_001286646.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.35
Genes affected
SLC45A4 (HGNC:29196): (solute carrier family 45 member 4) Predicted to enable sucrose:proton symporter activity. Predicted to be involved in sucrose transport. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC45A4 | NM_001286646.2 | c.-401+17880A>C | intron_variant | ENST00000517878.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A4 | ENST00000517878.6 | c.-401+17880A>C | intron_variant | 1 | NM_001286646.2 | ||||
ENST00000520606.1 | n.126-2478T>G | intron_variant, non_coding_transcript_variant | 5 | ||||||
SLC45A4 | ENST00000520137.1 | c.-339+17880A>C | intron_variant | 3 | |||||
SLC45A4 | ENST00000521804.1 | n.197+17880A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.275 AC: 41697AN: 151802Hom.: 6140 Cov.: 31
GnomAD3 genomes
?
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41697
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151802
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.275 AC: 41727AN: 151920Hom.: 6143 Cov.: 31 AF XY: 0.275 AC XY: 20422AN XY: 74246
GnomAD4 genome
?
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41727
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151920
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31
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20422
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74246
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810
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at