dbSNP rs104895065: RAD52:c.*317G>A (chr12-913074-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_134424.4(RAD52):c.*317G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.000019 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000015 ( 0 hom. )

Consequence

RAD52
NM_134424.4 3_prime_UTR

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -0.0730

Publications

2 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_134424.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RAD52	NM_134424.4	MANE Select	c.*317G>A	3_prime_UTR	Exon 12 of 12	NP_602296.2	Q5DR82
RAD52	NM_001297419.1		c.*317G>A	3_prime_UTR	Exon 12 of 12	NP_001284348.1	Q5DR82
RAD52	NM_001297421.2		c.*317G>A	3_prime_UTR	Exon 10 of 10	NP_001284350.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RAD52	ENST00000358495.8	TSL:1 MANE Select	c.*317G>A	3_prime_UTR	Exon 12 of 12	ENSP00000351284.3	P43351-1
RAD52	ENST00000430095.6	TSL:1	c.*317G>A	3_prime_UTR	Exon 12 of 12	ENSP00000387901.2	P43351-1
RAD52	ENST00000904782.1		c.*317G>A	3_prime_UTR	Exon 12 of 12	ENSP00000574841.1

Frequencies

GnomAD3 genomes

AF:

0.0000192

AC:

AN:

52178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000474

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000154

AC:

AN:

130030

Hom.:

Cov.:

AF XY:

0.0000157

AC XY:

AN XY:

63796

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

4920

American (AMR)

AF:

0.00

AC:

AN:

4334

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6168

East Asian (EAS)

AF:

0.00

AC:

AN:

12730

South Asian (SAS)

AF:

0.00

AC:

AN:

4008

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4388

Middle Eastern (MID)

AF:

0.00

AC:

AN:

742

European-Non Finnish (NFE)

AF:

0.0000240

AC:

AN:

83182

Other (OTH)

AF:

0.00

AC:

AN:

9558

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000192

AC:

AN:

52178

Hom.:

Cov.:

AF XY:

0.0000393

AC XY:

AN XY:

25414

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

17970

American (AMR)

AF:

0.00

AC:

AN:

3956

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1266

East Asian (EAS)

AF:

0.00

AC:

AN:

1156

South Asian (SAS)

AF:

0.00

AC:

AN:

2194

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3374

Middle Eastern (MID)

AF:

0.00

AC:

AN:

170

European-Non Finnish (NFE)

AF:

0.0000474

AC:

AN:

21090

Other (OTH)

AF:

0.00

AC:

AN:

774

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

ClinVar submissions

Significance:not provided

Revision:no classification provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.9

(source)

DANN

Benign

0.54

PhyloP100

-0.073

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over