rs5763254

Positions:

• chr22-29467163-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

RFPL1S (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985541	XR_001755482.2	n.4434+970A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RFPL1S	ENST00000248980.9	n.271+5143A>G		intron_variant		1
RFPL1S	ENST00000461286.4	n.307+5143A>G		intron_variant		4
RFPL1S	ENST00000657516.1	n.593+10847A>G		intron_variant

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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.234

Alfa AF: 0.194 Hom.: 4113

Bravo AF: 0.257

Asia WGS AF: 0.353 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5763254; hg19: chr22-29863152;