12-913069-A-T

Variant names:

• chr12-913069-A-T
• rs104895061
• NM_134424.4:c.*322T>A

Variant summary

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

The NM_134424.4(RAD52):​c.*322T>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: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RAD52 NM_134424.4 3_prime_UTR
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.443
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAD52	NM_134424.4	MANE Select	c.*322T>A		3_prime_UTR	Exon 12 of 12	NP_602296.2	Q5DR82
	RAD52	NM_001297419.1		c.*322T>A		3_prime_UTR	Exon 12 of 12	NP_001284348.1	Q5DR82
	RAD52	NM_001297421.2		c.*322T>A		3_prime_UTR	Exon 10 of 10	NP_001284350.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAD52	ENST00000358495.8	TSL:1 MANE Select	c.*322T>A		3_prime_UTR	Exon 12 of 12	ENSP00000351284.3	P43351-1
	RAD52	ENST00000430095.6	TSL:1	c.*322T>A		3_prime_UTR	Exon 12 of 12	ENSP00000387901.2	P43351-1
	RAD52	ENST00000904782.1		c.*322T>A		3_prime_UTR	Exon 12 of 12	ENSP00000574841.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 41816 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20766

African (AFR) AF: 0.00 AC: 0 AN: 2086

American (AMR) AF: 0.00 AC: 0 AN: 1008

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2170

East Asian (EAS) AF: 0.00 AC: 0 AN: 3254

South Asian (SAS) AF: 0.00 AC: 0 AN: 1988

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1338

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 412

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 26410

Other (OTH) AF: 0.00 AC: 0 AN: 3150

GnomAD4 genome Cov.: 0

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.44

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

Other links and lift over

dbSNP: rs104895061; hg19: chr12-1022235;