22-29397652-A-G

Position:

• chr22-29397652-A-G

Variant summary

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

The NM_001393612.1(RFPL1):​c.-1210-9151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,178 control chromosomes in the GnomAD database, including 1,355 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 0.12 (1355 hom., cov: 32)
• Consequence: RFPL1 NM_001393612.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

Genes affected

RFPL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RFPL1	NM_001393612.1	c.-1210-9151A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650462.1	n.189-9151A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18914 AN: 152060 Hom.: 1353 Cov.: 32

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.124 AC: 18928 AN: 152178 Hom.: 1355 Cov.: 32 AF XY: 0.125 AC XY: 9308 AN XY: 74418

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.126

Alfa AF: 0.126 Hom.: 1820

Bravo AF: 0.122

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2267138; hg19: chr22-29793641;