rs842644
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001291746.2(REL):c.154-40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 1,233,650 control chromosomes in the GnomAD database, including 551,919 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.96 ( 70101 hom., cov: 32)
Exomes 𝑓: 0.94 ( 481818 hom. )
Consequence
REL
NM_001291746.2 intron
NM_001291746.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.224
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 2-60894357-G-A is Benign according to our data. Variant chr2-60894357-G-A is described in ClinVar as [Benign]. Clinvar id is 2688192.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REL | NM_001291746.2 | c.154-40G>A | intron_variant | ENST00000394479.4 | |||
REL | NM_002908.4 | c.154-40G>A | intron_variant | ||||
REL | XM_017004627.3 | c.154-40G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REL | ENST00000394479.4 | c.154-40G>A | intron_variant | 1 | NM_001291746.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.959 AC: 145965AN: 152172Hom.: 70048 Cov.: 32
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GnomAD3 exomes AF: 0.949 AC: 159389AN: 167920Hom.: 75720 AF XY: 0.950 AC XY: 86621AN XY: 91144
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GnomAD4 exome AF: 0.944 AC: 1020470AN: 1081360Hom.: 481818 Cov.: 13 AF XY: 0.944 AC XY: 507987AN XY: 537944
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GnomAD4 genome ? AF: 0.959 AC: 146077AN: 152290Hom.: 70101 Cov.: 32 AF XY: 0.959 AC XY: 71389AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 99% of patients studied by a panel of primary immunodeficiencies. Number of patients: 94. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at