XM_047445730.1:c.-12222A>G

Variant names:

• chr2-17532533-T-C
• rs424827
• XM_047445730.1:c.-12222A>G

Variant summary

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

The XM_047445730.1(RAD51AP2):​c.-12222A>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,832 control chromosomes in the GnomAD database, including 26,902 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 0.56 (26902 hom., cov: 31)
• Consequence: RAD51AP2 XM_047445730.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 7 publications found

Genes affected

RAD51AP2 (HGNC:34417): (RAD51 associated protein 2) Predicted to enable double-stranded DNA binding activity and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair via homologous recombination and interstrand cross-link repair. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000308172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832128.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308172	ENST00000832128.1		n.291+13605T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85265 AN: 151716 Hom.: 26895 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.562 AC: 85294 AN: 151832 Hom.: 26902 Cov.: 31 AF XY: 0.571 AC XY: 42382 AN XY: 74190

African (AFR) AF: 0.257 AC: 10617 AN: 41334

American (AMR) AF: 0.683 AC: 10418 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4574 AN: 5166

South Asian (SAS) AF: 0.809 AC: 3892 AN: 4812

European-Finnish (FIN) AF: 0.690 AC: 7266 AN: 10538

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44202 AN: 67946

Other (OTH) AF: 0.612 AC: 1288 AN: 2104

Alfa AF: 0.635 Hom.: 15820

Bravo AF: 0.548

Asia WGS AF: 0.821 AC: 2851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.57
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs424827; hg19: chr2-17713800;