rs2612067

Positions:

• chr12-65776383-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026825.2(RPSAP52):​n.133-17352A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,120 control chromosomes in the GnomAD database, including 3,658 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 0.18 (3658 hom., cov: 32)
• Consequence: RPSAP52 NR_026825.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

Genes affected

RPSAP52 (HGNC:35752): (ribosomal protein SA pseudogene 52)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPSAP52	NR_026825.2	n.133-17352A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPSAP52	ENST00000489520.2	n.133-17352A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27741 AN: 152002 Hom.: 3641 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.183 AC: 27801 AN: 152120 Hom.: 3658 Cov.: 32 AF XY: 0.181 AC XY: 13494 AN XY: 74360

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.186

Alfa AF: 0.120 Hom.: 2570

Bravo AF: 0.194

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2612067; hg19: chr12-66170163;