rs7286017

chr22-32365728-G-C

Variant summary

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

The NR_104232.1(RFPL3S):n.206+1962C>G variant causes a intron, non coding transcript 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 NR_104232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

RFPL3S (HGNC:9981): (RFPL3 antisense)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RFPL3S	NR_104232.1	n.206+1962C>G		intron_variant, non_coding_transcript_variant
RFPL3S	NR_001450.3	n.274+1962C>G		intron_variant, non_coding_transcript_variant
RFPL3S	NR_002596.2	n.274+1962C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RFPL3S	ENST00000655996.1	n.415+1962C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0688

Gnomad4 EAS AF: 0.00366

Gnomad4 SAS AF: 0.0815

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0502

Gnomad4 OTH AF: 0.0625

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7286017; hg19: chr22-32761715;