rs5030490
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001377277.1(RAG1):c.-289+2098T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 152,310 control chromosomes in the GnomAD database, including 35 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 0.013 ( 35 hom., cov: 33)
Consequence
RAG1
NM_001377277.1 intron
NM_001377277.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.08
Genes affected
RAG1 (HGNC:9831): (recombination activating 1) The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires RAG2. Defects in this gene can be the cause of several diseases. [provided by RefSeq, Jul 2008]
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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 (EAS) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAG1 | NM_001377277.1 | c.-289+2098T>C | intron_variant | ||||
RAG1 | NM_001377278.1 | c.-227+2098T>C | intron_variant | ||||
RAG1 | NM_001377279.1 | c.-129+2098T>C | intron_variant | ||||
RAG1 | NM_001377280.1 | c.-15+2098T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAG1 | ENST00000697713.1 | c.-131+2098T>C | intron_variant | P1 | |||||
RAG1 | ENST00000697714.1 | c.-15+2098T>C | intron_variant | P1 | |||||
RAG1 | ENST00000697715.1 | c.-289+2098T>C | intron_variant | P1 | |||||
RAG1 | ENST00000529126.5 | n.330+1597T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0134 AC: 2044AN: 152192Hom.: 35 Cov.: 33
GnomAD3 genomes
?
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2044
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152192
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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: 0.0134 AC: 2044AN: 152310Hom.: 35 Cov.: 33 AF XY: 0.0131 AC XY: 977AN XY: 74466
GnomAD4 genome
?
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2044
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152310
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33
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977
AN XY:
74466
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115
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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