rs12412095

chr10-6071560-A-Gchr10-6071560-A-T

Variant summary

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

The ENST00000397237.2(RPL32P23):n.359T>C 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 0.255 in 152,776 control chromosomes in the GnomAD database, including 5,672 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 0.26 (5639 hom., cov: 31)
  • Exomes 𝑓: 0.25 (33 hom.)
• Consequence: RPL32P23 ENST00000397237.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56

Genes affected

RPL32P23 (HGNC:36007): (ribosomal protein L32 pseudogene 23)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL32P23	ENST00000397237.2	n.359T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38660 AN: 151546 Hom.: 5629 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.247

GnomAD4 exome AF: 0.251 AC: 279 AN: 1110 Hom.: 33 Cov.: 0 AF XY: 0.265 AC XY: 179 AN XY: 676

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.0946

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.145

Gnomad4 SAS exome AF: 0.212

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.255 AC: 38683 AN: 151666 Hom.: 5639 Cov.: 31 AF XY: 0.257 AC XY: 19044 AN XY: 74124

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.250

Alfa AF: 0.278 Hom.: 4853

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	1.1
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12412095; hg19: chr10-6113523;