rs2331703

Variant summary

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

The NM_133510.4(RAD51B):​c.958-28123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,258 control chromosomes in the GnomAD database, including 55,397 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 0.85 ( 55397 hom., cov: 32)

Consequence

RAD51B
NM_133510.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.521
Variant links:
Genes affected
RAD51B (HGNC:9822): (RAD51 paralog B) The protein encoded by this gene is a member of the RAD51 protein family. RAD51 family members are evolutionarily conserved proteins essential for DNA repair by homologous recombination. This protein has been shown to form a stable heterodimer with the family member RAD51C, which further interacts with the other family members, such as RAD51, XRCC2, and XRCC3. Overexpression of this gene was found to cause cell cycle G1 delay and cell apoptosis, which suggested a role of this protein in sensing DNA damage. Rearrangements between this locus and high mobility group AT-hook 2 (HMGA2, GeneID 8091) have been observed in uterine leiomyomata. [provided by RefSeq, Mar 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAD51BNM_133510.4 linkuse as main transcriptc.958-28123C>T intron_variant ENST00000471583.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAD51BENST00000471583.6 linkuse as main transcriptc.958-28123C>T intron_variant 1 NM_133510.4 P4O15315-2

Frequencies

GnomAD3 genomes
AF:
0.851
AC:
129416
AN:
152140
Hom.:
55329
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.935
Gnomad AMI
AF:
0.784
Gnomad AMR
AF:
0.847
Gnomad ASJ
AF:
0.730
Gnomad EAS
AF:
0.968
Gnomad SAS
AF:
0.804
Gnomad FIN
AF:
0.827
Gnomad MID
AF:
0.731
Gnomad NFE
AF:
0.807
Gnomad OTH
AF:
0.808
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.851
AC:
129546
AN:
152258
Hom.:
55397
Cov.:
32
AF XY:
0.850
AC XY:
63307
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.935
Gnomad4 AMR
AF:
0.847
Gnomad4 ASJ
AF:
0.730
Gnomad4 EAS
AF:
0.968
Gnomad4 SAS
AF:
0.805
Gnomad4 FIN
AF:
0.827
Gnomad4 NFE
AF:
0.807
Gnomad4 OTH
AF:
0.810
Alfa
AF:
0.850
Hom.:
10269
Bravo
AF:
0.855
Asia WGS
AF:
0.897
AC:
3120
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
6.1
DANN
Benign
0.73

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: rs2331703; hg19: chr14-68906766; API