chr14-68495787-T-G

Variant summary

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

The ENST00000487861.5(RAD51B):​c.1036+27537T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,102 control chromosomes in the GnomAD database, including 1,740 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 0.13 ( 1740 hom., cov: 32)

Consequence

RAD51B
ENST00000487861.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.361
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]

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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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAD51BNM_001321809.2 linkuse as main transcriptc.1036+27537T>G intron_variant NP_001308738.1
RAD51BNM_001321810.2 linkuse as main transcriptc.1036+27537T>G intron_variant NP_001308739.1
RAD51BNM_001321812.1 linkuse as main transcriptc.1036+27537T>G intron_variant NP_001308741.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAD51BENST00000487270.5 linkuse as main transcriptc.1036+27537T>G intron_variant 1 ENSP00000419471 O15315-3
RAD51BENST00000487861.5 linkuse as main transcriptc.1036+27537T>G intron_variant 1 ENSP00000419881
RAD51BENST00000488612.5 linkuse as main transcriptc.1036+27537T>G intron_variant 1 ENSP00000420061 O15315-4

Frequencies

GnomAD3 genomes
AF:
0.130
AC:
19819
AN:
151984
Hom.:
1740
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0675
Gnomad AMI
AF:
0.177
Gnomad AMR
AF:
0.154
Gnomad ASJ
AF:
0.117
Gnomad EAS
AF:
0.517
Gnomad SAS
AF:
0.147
Gnomad FIN
AF:
0.170
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.127
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.130
AC:
19833
AN:
152102
Hom.:
1740
Cov.:
32
AF XY:
0.134
AC XY:
9971
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0675
Gnomad4 AMR
AF:
0.155
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.516
Gnomad4 SAS
AF:
0.148
Gnomad4 FIN
AF:
0.170
Gnomad4 NFE
AF:
0.127
Gnomad4 OTH
AF:
0.131
Alfa
AF:
0.130
Hom.:
908
Bravo
AF:
0.130
Asia WGS
AF:
0.306
AC:
1062
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.3
DANN
Benign
0.64

Splicing

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: rs3784131; hg19: chr14-68962504; API