rs7286017

Variant names:

• chr22-32365728-G-C
• rs7286017
• ENST00000382084.10:n.241+1962C>G

Variant summary

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

The ENST00000658273.1(RFPL3S):​n.830C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0649 in 152,158 control chromosomes in the GnomAD database, including 387 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 0.065 (387 hom., cov: 32)
• Consequence: RFPL3S ENST00000658273.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

Genes affected

RFPL3S (HGNC:9981): (RFPL3 antisense)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658273.1. 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
	RFPL3S	NR_001450.3		n.274+1962C>G		intron	N/A
	RFPL3S	NR_002596.2		n.274+1962C>G		intron	N/A
	RFPL3S	NR_104232.1		n.206+1962C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFPL3S	ENST00000382084.10	TSL:1	n.241+1962C>G		intron	N/A
	RFPL3S	ENST00000400234.6	TSL:1	n.274+1962C>G		intron	N/A
	RFPL3S	ENST00000658273.1		n.830C>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9861 AN: 152040 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0688

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0649 AC: 9868 AN: 152158 Hom.: 387 Cov.: 32 AF XY: 0.0636 AC XY: 4730 AN XY: 74392

African (AFR) AF: 0.108 AC: 4472 AN: 41484

American (AMR) AF: 0.0556 AC: 850 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0688 AC: 239 AN: 3472

East Asian (EAS) AF: 0.00366 AC: 19 AN: 5186

South Asian (SAS) AF: 0.0815 AC: 392 AN: 4812

European-Finnish (FIN) AF: 0.0288 AC: 305 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0502 AC: 3414 AN: 68012

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0605 Hom.: 52

Bravo AF: 0.0671

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7286017;

hg19: chr22-32761715;