rs12312907

Positions:

• chr12-110841836-C-T

Variant summary

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

The ENST00000465069.2(RPL29P25):​n.552G>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 0.0501 in 957,436 control chromosomes in the GnomAD database, including 1,705 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 0.071 (548 hom., cov: 32)
  • Exomes 𝑓: 0.046 (1157 hom.)
• Consequence: RPL29P25 ENST00000465069.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

Genes affected

RPL29P25 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL29P25		n.110841836C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL29P25	ENST00000465069.2	n.552G>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000257268	ENST00000551161.1	n.217-3763C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10858 AN: 152046 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0368

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0431

Gnomad OTH AF: 0.0664

GnomAD4 exome AF: 0.0461 AC: 37115 AN: 805272 Hom.: 1157 Cov.: 11 AF XY: 0.0457 AC XY: 18966 AN XY: 415244

Gnomad4 AFR exome AF: 0.153

Gnomad4 AMR exome AF: 0.0390

Gnomad4 ASJ exome AF: 0.0320

Gnomad4 EAS exome AF: 0.000311

Gnomad4 SAS exome AF: 0.0412

Gnomad4 FIN exome AF: 0.0709

Gnomad4 NFE exome AF: 0.0445

Gnomad4 OTH exome AF: 0.0518

GnomAD4 genome AF: 0.0714 AC: 10866 AN: 152164 Hom.: 548 Cov.: 32 AF XY: 0.0692 AC XY: 5150 AN XY: 74388

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0456

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0371

Gnomad4 FIN AF: 0.0727

Gnomad4 NFE AF: 0.0431

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0582 Hom.: 39

Bravo AF: 0.0732

Asia WGS AF: 0.0260 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
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: rs12312907; hg19: chr12-111279640;