rs12530

chr22-32387917-T-C

Variant summary

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

The NM_014306.5(RTCB):c.*75A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 979,458 control chromosomes in the GnomAD database, including 13,715 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 0.12 (1576 hom., cov: 33)
  • Exomes 𝑓: 0.16 (12139 hom.)
• Consequence: RTCB NM_014306.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

Genes affected

RTCB (HGNC:26935): (RNA 2',3'-cyclic phosphate and 5'-OH ligase) Enables RNA ligase (ATP) activity and vinculin binding activity. Involved in tRNA splicing, via endonucleolytic cleavage and ligation. Located in cytosol and nucleoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RTCB	NM_014306.5	c.*75A>G		3_prime_UTR_variant	12/12	ENST00000216038.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RTCB	ENST00000216038.6	c.*75A>G		3_prime_UTR_variant	12/12	1	NM_014306.5	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18935 AN: 152188 Hom.: 1575 Cov.: 33

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.159 AC: 131416 AN: 827152 Hom.: 12139 Cov.: 11 AF XY: 0.155 AC XY: 67378 AN XY: 433650

Gnomad4 AFR exome AF: 0.0301

Gnomad4 AMR exome AF: 0.0737

Gnomad4 ASJ exome AF: 0.127

Gnomad4 EAS exome AF: 0.000166

Gnomad4 SAS exome AF: 0.0629

Gnomad4 FIN exome AF: 0.204

Gnomad4 NFE exome AF: 0.192

Gnomad4 OTH exome AF: 0.141

GnomAD4 genome AF: 0.124 AC: 18936 AN: 152306 Hom.: 1576 Cov.: 33 AF XY: 0.123 AC XY: 9160 AN XY: 74468

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.0893

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0646

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.110

Alfa AF: 0.140 Hom.: 349

Bravo AF: 0.112

Asia WGS AF: 0.0390 AC: 135 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	0.88
Dann	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12530; hg19: chr22-32783904; COSMIC: COSV53281178; COSMIC: COSV53281178;