dbSNP rs11226: RAD52:c.*744C>T (chr12-912647-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_134424.4(RAD52):c.*744C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 171,536 control chromosomes in the GnomAD database, including 16,526 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 0.44 ( 14326 hom., cov: 24)

Exomes 𝑓: 0.42 ( 2200 hom. )

Consequence

RAD52
NM_134424.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

Publications

22 publications found

Variant links:

Genes affected

RAD52 (HGNC:9824): (RAD52 homolog, DNA repair protein) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Rad52, a protein important for DNA double-strand break repair and homologous recombination. This gene product was shown to bind single-stranded DNA ends, and mediate the DNA-DNA interaction necessary for the annealing of complementary DNA strands. It was also found to interact with DNA recombination protein RAD51, which suggested its role in RAD51 related DNA recombination and repair. A pseudogene of this gene is present on chromosome 2. Alternative splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Jul 2014]

RAD52 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD52	NM_134424.4 link	c.*744C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000358495.8	NP_602296.2	P43351-1Q5DR82

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD52	ENST00000358495.8 link	c.*744C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_134424.4	ENSP00000351284.3		P43351-1

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

64456

AN:

147892

Hom.:

14309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.528

Gnomad AMR

AF:

0.519

Gnomad ASJ

AF:

0.404

Gnomad EAS

AF:

0.531

Gnomad SAS

AF:

0.334

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.416

GnomAD4 exome

AF:

0.417

AC:

9817

AN:

23550

Hom.:

2200

Cov.:

AF XY:

0.413

AC XY:

4445

AN XY:

10762

show subpopulations

African (AFR)

AF:

0.357

AC:

291

AN:

816

American (AMR)

AF:

0.510

AC:

252

AN:

494

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

573

AN:

1484

East Asian (EAS)

AF:

0.480

AC:

2397

AN:

4990

South Asian (SAS)

AF:

0.321

AC:

AN:

190

European-Finnish (FIN)

AF:

0.286

AC:

AN:

Middle Eastern (MID)

AF:

0.195

AC:

AN:

164

European-Non Finnish (NFE)

AF:

0.403

AC:

5419

AN:

13456

Other (OTH)

AF:

0.406

AC:

788

AN:

1942

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

229

458

686

915

1144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

176

220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.436

AC:

64497

AN:

147986

Hom.:

14326

Cov.:

AF XY:

0.437

AC XY:

31382

AN XY:

71852

show subpopulations

African (AFR)

AF:

0.376

AC:

15081

AN:

40078

American (AMR)

AF:

0.519

AC:

7638

AN:

14714

Ashkenazi Jewish (ASJ)

AF:

0.404

AC:

1396

AN:

3458

East Asian (EAS)

AF:

0.531

AC:

2665

AN:

5020

South Asian (SAS)

AF:

0.333

AC:

1568

AN:

4708

European-Finnish (FIN)

AF:

0.452

AC:

4258

AN:

9418

Middle Eastern (MID)

AF:

0.278

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.453

AC:

30491

AN:

67364

Other (OTH)

AF:

0.414

AC:

842

AN:

2032

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1647

3294

4940

6587

8234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.441

Hom.:

2440

Bravo

AF:

0.441

Asia WGS

AF:

0.410

AC:

1425

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

(source)

DANN

Benign

0.69

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over