12-110841831-C-T

Variant names:

• chr12-110841831-C-T
• rs12312903
• ENST00000465069.2:n.557G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000465069.2(RPL29P25):​n.557G>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 0.0508 in 867,942 control chromosomes in the GnomAD database, including 1,591 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 (550 hom., cov: 32)
  • Exomes 𝑓: 0.046 (1041 hom.)
• Consequence: RPL29P25 ENST00000465069.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 0 publications found

Genes affected

RPL29P25 (HGNC:37039): (ribosomal protein L29 pseudogene 25)

ENSG00000257268 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465069.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL29P25	ENST00000465069.2	TSL:6	n.557G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000257268	ENST00000551161.1	TSL:3	n.217-3768C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10862 AN: 152078 Hom.: 549 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0431

Gnomad OTH AF: 0.0665

GnomAD4 exome AF: 0.0464 AC: 33188 AN: 715746 Hom.: 1041 Cov.: 9 AF XY: 0.0457 AC XY: 17039 AN XY: 372986

African (AFR) AF: 0.154 AC: 2619 AN: 17052

American (AMR) AF: 0.0388 AC: 1019 AN: 26230

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 484 AN: 15420

East Asian (EAS) AF: 0.000126 AC: 4 AN: 31720

South Asian (SAS) AF: 0.0414 AC: 1793 AN: 43342

European-Finnish (FIN) AF: 0.0703 AC: 2202 AN: 31302

Middle Eastern (MID) AF: 0.0718 AC: 172 AN: 2396

European-Non Finnish (NFE) AF: 0.0450 AC: 23126 AN: 514138

Other (OTH) AF: 0.0518 AC: 1769 AN: 34146

GnomAD4 genome AF: 0.0714 AC: 10870 AN: 152196 Hom.: 550 Cov.: 32 AF XY: 0.0692 AC XY: 5151 AN XY: 74404

African (AFR) AF: 0.145 AC: 5995 AN: 41480

American (AMR) AF: 0.0456 AC: 698 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4820

European-Finnish (FIN) AF: 0.0726 AC: 770 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0431 AC: 2931 AN: 68018

Other (OTH) AF: 0.0658 AC: 139 AN: 2112

Alfa AF: 0.0549 Hom.: 39

Bravo AF: 0.0732

Asia WGS AF: 0.0260 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12312903;

hg19: chr12-111279635;