rs10193964
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001291746.2(REL):c.303-1463A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,328 control chromosomes in the GnomAD database, including 3,427 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 0.20 ( 3420 hom., cov: 32)
Exomes 𝑓: 0.31 ( 7 hom. )
Consequence
REL
NM_001291746.2 intron
NM_001291746.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.71
Genes affected
REL (HGNC:9954): (REL proto-oncogene, NF-kB subunit) This gene encodes a protein that belongs to the Rel homology domain/immunoglobulin-like fold, plexin, transcription factor (RHD/IPT) family. Members of this family regulate genes involved in apoptosis, inflammation, the immune response, and oncogenic processes. This proto-oncogene plays a role in the survival and proliferation of B lymphocytes. Mutation or amplification of this gene is associated with B-cell lymphomas, including Hodgkin's lymphoma. Single nucleotide polymorphisms in this gene are associated with susceptibility to ulcerative colitis and rheumatoid arthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REL | NM_001291746.2 | c.303-1463A>G | intron_variant | ENST00000394479.4 | |||
REL | NM_002908.4 | c.303-1463A>G | intron_variant | ||||
REL | XM_017004627.3 | c.303-1463A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REL | ENST00000394479.4 | c.303-1463A>G | intron_variant | 1 | NM_001291746.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.203 AC: 30939AN: 152060Hom.: 3421 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.313 AC: 47AN: 150Hom.: 7 Cov.: 0 AF XY: 0.345 AC XY: 29AN XY: 84
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GnomAD4 genome ? AF: 0.203 AC: 30945AN: 152178Hom.: 3420 Cov.: 32 AF XY: 0.202 AC XY: 15007AN XY: 74390
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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