GeneBe

ENST00000533482.5:n.-1C>T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000533482.5(RAD50):​n.-388C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RAD50
ENST00000533482.5 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.168

Publications

0 publications found
Variant links:
Genes affected
RAD50 (HGNC:9816): (RAD50 double strand break repair protein) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Rad50, a protein involved in DNA double-strand break repair. This protein forms a complex with MRE11 and NBS1. The protein complex binds to DNA and displays numerous enzymatic activities that are required for nonhomologous joining of DNA ends. This protein, cooperating with its partners, is important for DNA double-strand break repair, cell cycle checkpoint activation, telomere maintenance, and meiotic recombination. Knockout studies of the mouse homolog suggest this gene is essential for cell growth and viability. Mutations in this gene are the cause of Nijmegen breakage syndrome-like disorder.[provided by RefSeq, Apr 2010]
IL5 (HGNC:6016): (interleukin 5) This gene encodes a cytokine that acts as a growth and differentiation factor for both B cells and eosinophils. The encoded cytokine plays a major role in the regulation of eosinophil formation, maturation, recruitment and survival. The increased production of this cytokine may be related to pathogenesis of eosinophil-dependent inflammatory diseases. This cytokine functions by binding to its receptor, which is a heterodimer, whose beta subunit is shared with the receptors for interleukine 3 (IL3) and colony stimulating factor 2 (CSF2/GM-CSF). This gene is located on chromosome 5 within a cytokine gene cluster which includes interleukin 4 (IL4), interleukin 13 (IL13), and CSF2 . This gene, IL4, and IL13 may be regulated coordinately by long-range regulatory elements spread over 120 kilobases on chromosome 5q31. [provided by RefSeq, Jul 2013]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RAD50NM_005732.4 linkc.-388C>T upstream_gene_variant ENST00000378823.8 NP_005723.2 Q92878-1A5D6Y3
IL5XM_005271988.5 linkc.-222G>A upstream_gene_variant XP_005272045.1
IL5XM_011543373.4 linkc.-390G>A upstream_gene_variant XP_011541675.1 P05113
IL5XM_047417148.1 linkc.-222G>A upstream_gene_variant XP_047273104.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000283782ENST00000638452.2 linkc.-168-2347C>T intron_variant Intron 3 of 26 5 ENSP00000492349.2 A0A1W2PQ90
RAD50ENST00000378823.8 linkc.-388C>T upstream_gene_variant 1 NM_005732.4 ENSP00000368100.4 Q92878-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1040304
Hom.:
0
Cov.:
15
AF XY:
0.00
AC XY:
0
AN XY:
498664
African (AFR)
AF:
0.00
AC:
0
AN:
23348
American (AMR)
AF:
0.00
AC:
0
AN:
12158
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14208
East Asian (EAS)
AF:
0.00
AC:
0
AN:
21892
South Asian (SAS)
AF:
0.00
AC:
0
AN:
55802
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10312
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2648
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
858822
Other (OTH)
AF:
0.00
AC:
0
AN:
41114
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
6.8
DANN
Benign
0.95
PhyloP100
-0.17
PromoterAI
-0.092
Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

hg19: chr5-131892629; API