rs13053817

chr22-29451733-C-A

Variant summary

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

The ENST00000248980.9(RFPL1S):n.272-12540G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RFPL1S	ENST00000461286.4	n.308-9604G>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0232

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.166

Alfa AF: 0.174 Hom.: 5611

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13053817; hg19: chr22-29847722;