rs13053624

Variant names:

• chr22-29442214-A-T
• rs13053624
• ENST00000354373.2:c.*92A>T

Variant summary

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

The ENST00000354373.2(RFPL1):​c.*92A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 892,150 control chromosomes in the GnomAD database, including 13,485 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 0.17 (2237 hom., cov: 32)
  • Exomes 𝑓: 0.17 (11248 hom.)
• Consequence: RFPL1 ENST00000354373.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 13 publications found

Genes affected

RFPL1 (HGNC:9977): (ret finger protein like 1) Predicted to enable ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of G2/M transition of mitotic cell cycle; negative regulation of cell division; and positive regulation of proteolysis. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RFPL1	NM_021026.2	c.*92A>T		3_prime_UTR_variant	Exon 2 of 2		NP_066306.2
RFPL1	NM_001393612.1	c.*92A>T		3_prime_UTR_variant	Exon 10 of 10		NP_001380541.1
RFPL1S	NR_002727.2	n.-85T>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFPL1	ENST00000354373.2	c.*92A>T		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000346342.2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25232 AN: 152020 Hom.: 2231 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.168 AC: 124621 AN: 740012 Hom.: 11248 Cov.: 10 AF XY: 0.166 AC XY: 61542 AN XY: 371052

African (AFR) AF: 0.199 AC: 3717 AN: 18638

American (AMR) AF: 0.0897 AC: 1761 AN: 19638

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 1267 AN: 14756

East Asian (EAS) AF: 0.0218 AC: 751 AN: 34472

South Asian (SAS) AF: 0.104 AC: 3796 AN: 36646

European-Finnish (FIN) AF: 0.148 AC: 6583 AN: 44556

Middle Eastern (MID) AF: 0.135 AC: 477 AN: 3530

European-Non Finnish (NFE) AF: 0.189 AC: 100838 AN: 532920

Other (OTH) AF: 0.156 AC: 5431 AN: 34856

GnomAD4 genome AF: 0.166 AC: 25273 AN: 152138 Hom.: 2237 Cov.: 32 AF XY: 0.160 AC XY: 11927 AN XY: 74370

African (AFR) AF: 0.195 AC: 8081 AN: 41470

American (AMR) AF: 0.101 AC: 1541 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.0233 AC: 121 AN: 5184

South Asian (SAS) AF: 0.105 AC: 506 AN: 4824

European-Finnish (FIN) AF: 0.151 AC: 1602 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12643 AN: 68000

Other (OTH) AF: 0.158 AC: 333 AN: 2110

Alfa AF: 0.183 Hom.: 300

Bravo AF: 0.164

Asia WGS AF: 0.0750 AC: 262 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	0.39
DANN	Benign	0.31
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13053624; hg19: chr22-29838203;