rs5763254

Variant names:

• chr22-29467163-T-C
• rs5763254
• ENST00000248980.9:n.271+5143A>G

Variant summary

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

The ENST00000248980.9(RFPL1S):​n.271+5143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 150,856 control chromosomes in the GnomAD database, including 5,492 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 0.25 (5492 hom., cov: 28)
• Consequence: RFPL1S ENST00000248980.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 5 publications found

Genes affected

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

LOC107985541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000248980.9. 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
	RFPL1S	ENST00000248980.9	TSL:1	n.271+5143A>G		intron	N/A
	RFPL1S	ENST00000461286.4	TSL:4	n.307+5143A>G		intron	N/A
	RFPL1S	ENST00000657516.2		n.593+10847A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.252 AC: 37982 AN: 150738 Hom.: 5483 Cov.: 28

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.252 AC: 38017 AN: 150856 Hom.: 5492 Cov.: 28 AF XY: 0.252 AC XY: 18564 AN XY: 73590

African (AFR) AF: 0.394 AC: 16162 AN: 40980

American (AMR) AF: 0.182 AC: 2744 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3454

East Asian (EAS) AF: 0.407 AC: 2084 AN: 5122

South Asian (SAS) AF: 0.285 AC: 1354 AN: 4754

European-Finnish (FIN) AF: 0.189 AC: 1965 AN: 10422

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12547 AN: 67788

Other (OTH) AF: 0.234 AC: 488 AN: 2086

Alfa AF: 0.199 Hom.: 5552

Bravo AF: 0.257

Asia WGS AF: 0.353 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.71
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs5763254; hg19: chr22-29863152;