rs1051672

Variant names:

• chr12-912391-G-A
• rs1051672
• NM_134424.4:c.*1000C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-912391-G-A
• chr12-912391-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_134424.4(RAD52):​c.*1000C>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 0.29 in 201,732 control chromosomes in the GnomAD database, including 9,014 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 0.30 (7213 hom., cov: 31)
  • Exomes 𝑓: 0.27 (1801 hom.)
• Consequence: RAD52 NM_134424.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 8 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

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.*1000C>T		3_prime_UTR	Exon 12 of 12	NP_602296.2	Q5DR82
	RAD52	NM_001297419.1		c.*1000C>T		3_prime_UTR	Exon 12 of 12	NP_001284348.1	Q5DR82
	RAD52	NM_001297421.2		c.*1000C>T		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.*1000C>T		3_prime_UTR	Exon 12 of 12	ENSP00000351284.3	P43351-1
	RAD52	ENST00000904779.1		c.*1000C>T		3_prime_UTR	Exon 12 of 12	ENSP00000574838.1
	RAD52	ENST00000904778.1		c.*1000C>T		3_prime_UTR	Exon 12 of 12	ENSP00000574837.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45063 AN: 151820 Hom.: 7205 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.267 AC: 13303 AN: 49794 Hom.: 1801 Cov.: 0 AF XY: 0.270 AC XY: 6250 AN XY: 23118

African (AFR) AF: 0.408 AC: 870 AN: 2130

American (AMR) AF: 0.238 AC: 334 AN: 1404

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 992 AN: 3214

East Asian (EAS) AF: 0.220 AC: 1760 AN: 8006

South Asian (SAS) AF: 0.309 AC: 134 AN: 434

European-Finnish (FIN) AF: 0.265 AC: 9 AN: 34

Middle Eastern (MID) AF: 0.355 AC: 118 AN: 332

European-Non Finnish (NFE) AF: 0.266 AC: 7990 AN: 30076

Other (OTH) AF: 0.263 AC: 1096 AN: 4164

GnomAD4 genome AF: 0.297 AC: 45110 AN: 151938 Hom.: 7213 Cov.: 31 AF XY: 0.294 AC XY: 21828 AN XY: 74222

African (AFR) AF: 0.417 AC: 17269 AN: 41430

American (AMR) AF: 0.256 AC: 3905 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1100 AN: 3460

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5176

South Asian (SAS) AF: 0.322 AC: 1550 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 1987 AN: 10538

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17413 AN: 67944

Other (OTH) AF: 0.312 AC: 659 AN: 2112

Alfa AF: 0.273 Hom.: 2703

Bravo AF: 0.305

Asia WGS AF: 0.293 AC: 1020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.54
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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: rs1051672; hg19: chr12-1021557;