rs1053872

Variant names:

• chr9-4860643-G-C
• rs1053872
• NM_005772.5:c.*368G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-4860643-G-C
• chr9-4860643-G-T

Variant summary

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

The NM_005772.5(RCL1):​c.*368G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 186,736 control chromosomes in the GnomAD database, including 9,222 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 0.30 (8346 hom., cov: 33)
  • Exomes 𝑓: 0.20 (876 hom.)
• Consequence: RCL1 NM_005772.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515

Genes affected

RCL1 (HGNC:17687): (RNA terminal phosphate cyclase like 1) Predicted to enable endoribonuclease activity. Predicted to be involved in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleoplasm. Predicted to be active in nucleolus. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCL1	NM_005772.5	c.*368G>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000381750.9	NP_005763.3
RCL1	NM_001286699.2	c.*368G>C		3_prime_UTR_variant	Exon 7 of 7		NP_001273628.1
RCL1	NM_001286700.2	c.*368G>C		3_prime_UTR_variant	Exon 8 of 8		NP_001273629.1
RCL1	NM_001286701.2	c.*368G>C		3_prime_UTR_variant	Exon 5 of 5		NP_001273630.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCL1	ENST00000381750.9	c.*368G>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_005772.5	ENSP00000371169.4

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45451 AN: 151938 Hom.: 8324 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.200 AC: 6952 AN: 34680 Hom.: 876 Cov.: 0 AF XY: 0.197 AC XY: 3477 AN XY: 17686

Gnomad4 AFR exome AF: 0.460

Gnomad4 AMR exome AF: 0.233

Gnomad4 ASJ exome AF: 0.178

Gnomad4 EAS exome AF: 0.490

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.215

Gnomad4 NFE exome AF: 0.185

Gnomad4 OTH exome AF: 0.208

GnomAD4 genome AF: 0.299 AC: 45516 AN: 152056 Hom.: 8346 Cov.: 33 AF XY: 0.296 AC XY: 22014 AN XY: 74324

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.255

Alfa AF: 0.119 Hom.: 183

Bravo AF: 0.312

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.53

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: rs1053872; hg19: chr9-4860643; COSMIC: COSV67754426; COSMIC: COSV67754426;