rs12460483

chr19-7665708-G-Achr19-7665708-G-C

Variant summary

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

The XR_007067117.1(RPS27AP19):n.30G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 279,458 control chromosomes in the GnomAD database, including 937 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 0.089 (803 hom., cov: 32)
  • Exomes 𝑓: 0.039 (134 hom.)
• Consequence: RPS27AP19 XR_007067117.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

RPS27AP19 (HGNC:52298): (RPS27A pseudogene 19)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS27AP19	XR_007067117.1	n.30G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS27AP19	ENST00000597285.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13556 AN: 152006 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0944

GnomAD4 exome AF: 0.0391 AC: 4973 AN: 127334 Hom.: 134 Cov.: 0 AF XY: 0.0391 AC XY: 3000 AN XY: 76694

Gnomad4 AFR exome AF: 0.00491

Gnomad4 AMR exome AF: 0.0602

Gnomad4 ASJ exome AF: 0.0429

Gnomad4 EAS exome AF: 0.00528

Gnomad4 SAS exome AF: 0.0459

Gnomad4 FIN exome AF: 0.0501

Gnomad4 NFE exome AF: 0.0376

Gnomad4 OTH exome AF: 0.0344

GnomAD4 genome AF: 0.0891 AC: 13561 AN: 152124 Hom.: 803 Cov.: 32 AF XY: 0.0896 AC XY: 6660 AN XY: 74370

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0930

Alfa AF: 0.0647 Hom.: 95

Bravo AF: 0.0895

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12460483; hg19: chr19-7730594;