chr2-17532533-T-C

Position:

• chr2-17532533-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD51AP2	XM_047445730.1	c.-12222A>G		5_prime_UTR_premature_start_codon_gain_variant	1/6		XP_047301686.1
RAD51AP2	XM_047445730.1	c.-12222A>G		5_prime_UTR_variant	1/6		XP_047301686.1
RAD51AP2	XM_024453116.2	c.-409-2119A>G		intron_variant			XP_024308884.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.612

Alfa AF: 0.634 Hom.: 14187

Bravo AF: 0.548

Asia WGS AF: 0.821 AC: 2851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs424827; hg19: chr2-17713800;