rs2039461
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_017014592.2(SLC24A2):c.-528-141603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,902 control chromosomes in the GnomAD database, including 18,399 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 0.44 ( 18399 hom., cov: 31)
Consequence
SLC24A2
XM_017014592.2 intron
XM_017014592.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.565
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 (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC24A2 | XM_017014592.2 | c.-528-141603A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.445 AC: 67588AN: 151786Hom.: 18403 Cov.: 31
GnomAD3 genomes
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67588
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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: 0.445 AC: 67572AN: 151902Hom.: 18399 Cov.: 31 AF XY: 0.436 AC XY: 32349AN XY: 74236
GnomAD4 genome
?
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AC:
67572
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151902
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Cov.:
31
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32349
AN XY:
74236
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Asia WGS
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AC:
922
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3464
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at