rs2040704

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005732.4(RAD50):​c.3475+285A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,758 control chromosomes in the GnomAD database, including 10,548 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.33 ( 10548 hom., cov: 31)

Consequence

RAD50
NM_005732.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0150
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 5-132637485-A-G is Benign according to our data. Variant chr5-132637485-A-G is described in ClinVar as [Benign]. Clinvar id is 1282436.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAD50NM_005732.4 linkuse as main transcriptc.3475+285A>G intron_variant ENST00000378823.8 NP_005723.2 Q92878-1A5D6Y3
TH2LCRRNR_132124.1 linkuse as main transcriptn.153+673T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAD50ENST00000378823.8 linkuse as main transcriptc.3475+285A>G intron_variant 1 NM_005732.4 ENSP00000368100.4 Q92878-1
ENSG00000283782ENST00000640655.2 linkuse as main transcriptc.3178+285A>G intron_variant 5 ENSP00000491596.2 A0A1W2PQ90

Frequencies

GnomAD3 genomes
AF:
0.327
AC:
49601
AN:
151642
Hom.:
10505
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.612
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.230
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.246
Gnomad FIN
AF:
0.242
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.221
Gnomad OTH
AF:
0.287
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.327
AC:
49692
AN:
151758
Hom.:
10548
Cov.:
31
AF XY:
0.325
AC XY:
24076
AN XY:
74178
show subpopulations
Gnomad4 AFR
AF:
0.612
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.230
Gnomad4 EAS
AF:
0.179
Gnomad4 SAS
AF:
0.246
Gnomad4 FIN
AF:
0.242
Gnomad4 NFE
AF:
0.221
Gnomad4 OTH
AF:
0.284
Alfa
AF:
0.230
Hom.:
5371
Bravo
AF:
0.337
Asia WGS
AF:
0.232
AC:
810
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJan 10, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.65
CADD
Benign
9.4
DANN
Benign
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2040704; hg19: chr5-131973177; API