rs2706347

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005732.4(RAD50):​c.214-6352G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,950 control chromosomes in the GnomAD database, including 9,350 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 0.31 ( 9350 hom., cov: 32)

Consequence

RAD50
NM_005732.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.342
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]

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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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAD50NM_005732.4 linkuse as main transcriptc.214-6352G>T intron_variant ENST00000378823.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAD50ENST00000378823.8 linkuse as main transcriptc.214-6352G>T intron_variant 1 NM_005732.4 P1Q92878-1

Frequencies

GnomAD3 genomes
AF:
0.311
AC:
47184
AN:
151832
Hom.:
9312
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.571
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.199
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.236
Gnomad FIN
AF:
0.231
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.311
AC:
47272
AN:
151950
Hom.:
9350
Cov.:
32
AF XY:
0.308
AC XY:
22902
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.572
Gnomad4 AMR
AF:
0.199
Gnomad4 ASJ
AF:
0.233
Gnomad4 EAS
AF:
0.177
Gnomad4 SAS
AF:
0.236
Gnomad4 FIN
AF:
0.231
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.268
Alfa
AF:
0.307
Hom.:
1622
Bravo
AF:
0.319
Asia WGS
AF:
0.227
AC:
791
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.25
DANN
Benign
0.48

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: rs2706347; hg19: chr5-131905117; API