rs4676049
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_047445367.1(RANBP2):c.8370+245755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,208 control chromosomes in the GnomAD database, including 1,894 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 0.13 ( 1894 hom., cov: 33)
Consequence
RANBP2
XM_047445367.1 intron
XM_047445367.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.48
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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP2 | XM_047445367.1 | c.8370+245755C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.131 AC: 19871AN: 152090Hom.: 1892 Cov.: 33
GnomAD3 genomes
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19871
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152090
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.131 AC: 19902AN: 152208Hom.: 1894 Cov.: 33 AF XY: 0.126 AC XY: 9405AN XY: 74438
GnomAD4 genome
?
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19902
AN:
152208
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Cov.:
33
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AC XY:
9405
AN XY:
74438
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Asia WGS
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512
AN:
3478
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