dbSNP rs7963551: RAD52:c.*1042A>C (chr12-912349-T-G) – 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.*1042A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 201,738 control chromosomes in the GnomAD database, including 2,112 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 ( 1566 hom., cov: 31)

Exomes 𝑓: 0.14 ( 546 hom. )

Consequence

RAD52
NM_134424.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.398

Publications

37 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD52	NM_134424.4 link	c.*1042A>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000358495.8	NP_602296.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD52	ENST00000358495.8 link	c.*1042A>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_134424.4	ENSP00000351284.3

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19977

AN:

151926

Hom.:

1563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0498

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.144

AC:

7153

AN:

49694

Hom.:

546

Cov.:

AF XY:

0.144

AC XY:

3336

AN XY:

23116

show subpopulations

African (AFR)

AF:

0.0406

AC:

AN:

2170

American (AMR)

AF:

0.124

AC:

176

AN:

1418

Ashkenazi Jewish (ASJ)

AF:

0.146

AC:

464

AN:

3182

East Asian (EAS)

AF:

0.137

AC:

1098

AN:

8014

South Asian (SAS)

AF:

0.153

AC:

AN:

418

European-Finnish (FIN)

AF:

0.188

AC:

AN:

Middle Eastern (MID)

AF:

0.232

AC:

AN:

310

European-Non Finnish (NFE)

AF:

0.151

AC:

4539

AN:

30024

Other (OTH)

AF:

0.157

AC:

646

AN:

4126

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

310

620

930

1240

1550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<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:

0.131

AC:

19986

AN:

152044

Hom.:

1566

Cov.:

AF XY:

0.136

AC XY:

10115

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.0500

AC:

2076

AN:

41508

American (AMR)

AF:

0.125

AC:

1915

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

543

AN:

3470

East Asian (EAS)

AF:

0.179

AC:

926

AN:

5170

South Asian (SAS)

AF:

0.166

AC:

798

AN:

4818

European-Finnish (FIN)

AF:

0.267

AC:

2816

AN:

10538

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10381

AN:

67962

Other (OTH)

AF:

0.132

AC:

279

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

869

1738

2607

3476

4345

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.141

Hom.:

324

Bravo

AF:

0.117

Asia WGS

AF:

0.154

AC:

538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

(source)

DANN

Benign

0.49

PhyloP100

-0.40

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