Variant chr14-67823747-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_133510.4(RAD51B):c.84+120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 729,970 control chromosomes in the GnomAD database, including 39,371 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8338 hom., cov: 32)

Exomes 𝑓: 0.32 ( 31033 hom. )

Consequence

RAD51B
NM_133510.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.907

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]

RAD51B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 14-67823747-G-A is Benign according to our data. Variant chr14-67823747-G-A is described in ClinVar as [Benign]. Clinvar id is 1271766.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD51B	NM_133510.4 link	c.84+120G>A		intron_variant		ENST00000471583.6	NP_598194.1	O15315-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51B	ENST00000471583.6 link	c.84+120G>A		intron_variant		1	NM_133510.4	ENSP00000418859.1		O15315-2

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49216

AN:

151930

Hom.:

8317

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.0750

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.354

Gnomad OTH

AF:

0.330

GnomAD4 exome

AF:

0.317

AC:

183403

AN:

577922

Hom.:

31033

AF XY:

0.315

AC XY:

94250

AN XY:

299270

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.219

Gnomad4 ASJ exome

AF:

0.389

Gnomad4 EAS exome

AF:

0.0868

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.286

Gnomad4 NFE exome

AF:

0.346

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.324

AC:

49270

AN:

152048

Hom.:

8338

Cov.:

AF XY:

0.316

AC XY:

23494

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.344

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.412

Gnomad4 EAS

AF:

0.0754

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.354

Gnomad4 OTH

AF:

0.326

Alfa

AF:

0.335

Hom.:

1052

Bravo

AF:

0.323

Asia WGS

AF:

0.179

AC:

622

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.79

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over