rs13053817

Variant names:

• chr22-29451733-C-A
• rs13053817
• ENST00000248980.9:n.272-12540G>T

Variant summary

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

The ENST00000248980.9(RFPL1S):​n.272-12540G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,044 control chromosomes in the GnomAD database, including 2,695 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 0.18 (2695 hom., cov: 31)
• Consequence: RFPL1S ENST00000248980.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 24 publications found

Genes affected

RFPL1S (HGNC:9978): (RFPL1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFPL1S	ENST00000248980.9	n.272-12540G>T		intron_variant	Intron 2 of 2	1
RFPL1S	ENST00000461286.4	n.308-9604G>T		intron_variant	Intron 2 of 2	4
RFPL1S	ENST00000657516.2	n.594-9604G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27285 AN: 151926 Hom.: 2686 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.168

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.180 AC: 27331 AN: 152044 Hom.: 2695 Cov.: 31 AF XY: 0.174 AC XY: 12898 AN XY: 74332

African (AFR) AF: 0.244 AC: 10107 AN: 41438

American (AMR) AF: 0.103 AC: 1575 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.0232 AC: 120 AN: 5180

South Asian (SAS) AF: 0.102 AC: 493 AN: 4820

European-Finnish (FIN) AF: 0.152 AC: 1606 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12635 AN: 67976

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.177 Hom.: 11954

Bravo AF: 0.179

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13053817; hg19: chr22-29847722;