rs3902093

Variant names:

• chr1-241832601-C-A
• rs3902093
• ENST00000414898.1:n.667C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

RPL6P3 (HGNC:35925): (ribosomal protein L6 pseudogene 3)

ENSG00000288723 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414898.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL6P3	ENST00000414898.1	TSL:6	n.667C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288723	ENST00000684005.2		n.168+15368G>T		intron	N/A

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

African (AFR) AF: 0.0448 AC: 715 AN: 15962

American (AMR) AF: 0.249 AC: 9732 AN: 39114

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 2527 AN: 18794

East Asian (EAS) AF: 0.139 AC: 4323 AN: 31208

South Asian (SAS) AF: 0.174 AC: 11602 AN: 66788

European-Finnish (FIN) AF: 0.137 AC: 6493 AN: 47410

Middle Eastern (MID) AF: 0.143 AC: 325 AN: 2272

European-Non Finnish (NFE) AF: 0.166 AC: 51834 AN: 311786

Other (OTH) AF: 0.156 AC: 4549 AN: 29162

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

African (AFR) AF: 0.0475 AC: 1971 AN: 41526

American (AMR) AF: 0.190 AC: 2901 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3470

East Asian (EAS) AF: 0.141 AC: 729 AN: 5174

South Asian (SAS) AF: 0.178 AC: 858 AN: 4822

European-Finnish (FIN) AF: 0.141 AC: 1486 AN: 10574

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11199 AN: 67972

Other (OTH) AF: 0.157 AC: 332 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs3902093; hg19: chr1-241995903;