rs3902093

Positions:

• chr1-241832601-C-A
• chr1-241832601-C-G
• chr1-241832601-C-T

Variant summary

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

The ENST00000414898.1(RPL6P3):​n.667C>A 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 0.157 in 714,626 control chromosomes in the GnomAD database, including 9,668 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 0.13 (1595 hom., cov: 32)
  • Exomes 𝑓: 0.16 (8073 hom.)
• Consequence: RPL6P3 ENST00000414898.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752

Genes affected

RPL6P3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL6P3		n.241832601C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL6P3	ENST00000414898.1	n.667C>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000288723	ENST00000684005.1	n.160+15368G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20112 AN: 152012 Hom.: 1585 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.164 AC: 92100 AN: 562496 Hom.: 8073 Cov.: 0 AF XY: 0.164 AC XY: 50515 AN XY: 307942

Gnomad4 AFR exome AF: 0.0448

Gnomad4 AMR exome AF: 0.249

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.139

Gnomad4 SAS exome AF: 0.174

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.132 AC: 20123 AN: 152130 Hom.: 1595 Cov.: 32 AF XY: 0.131 AC XY: 9740 AN XY: 74348

Gnomad4 AFR AF: 0.0475

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.157

Alfa AF: 0.115 Hom.: 240

Bravo AF: 0.135

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3902093; hg19: chr1-241995903;