rs7134682

chr12-65774371-G-T

Variant summary

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

The NR_026825.2(RPSAP52):n.133-15340C>A 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 0.355 in 152,152 control chromosomes in the GnomAD database, including 16,905 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 0.36 (16905 hom., cov: 33)
• Consequence: RPSAP52 NR_026825.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPSAP52	NR_026825.2	n.133-15340C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPSAP52	ENST00000489520.2	n.133-15340C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53897 AN: 152034 Hom.: 16843 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.355 AC: 54015 AN: 152152 Hom.: 16905 Cov.: 33 AF XY: 0.356 AC XY: 26466 AN XY: 74364

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.348

Alfa AF: 0.173 Hom.: 6478

Bravo AF: 0.380

Asia WGS AF: 0.511 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.3
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7134682; hg19: chr12-66168151;