ENST00000490908.1:n.-117A>G

Variant names:

• chr18-3406935-T-C
• rs7228082
• ENST00000490908.1:n.-117A>G

Variant summary

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

The ENST00000490908.1(RPL21P127):​n.-117A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 437,108 control chromosomes in the GnomAD database, including 9,043 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 0.22 (5354 hom., cov: 32)
  • Exomes 𝑓: 0.14 (3689 hom.)
• Consequence: RPL21P127 ENST00000490908.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 2 publications found

Genes affected

RPL21P127 (HGNC:36099): (ribosomal protein L21 pseudogene 127)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490908.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL21P127	ENST00000490908.1	TSL:6	n.-117A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33820 AN: 152042 Hom.: 5338 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.135 AC: 38530 AN: 284948 Hom.: 3689 AF XY: 0.130 AC XY: 19972 AN XY: 153482

African (AFR) AF: 0.433 AC: 3532 AN: 8150

American (AMR) AF: 0.387 AC: 5307 AN: 13716

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 1196 AN: 8108

East Asian (EAS) AF: 0.140 AC: 2273 AN: 16246

South Asian (SAS) AF: 0.0852 AC: 2905 AN: 34114

European-Finnish (FIN) AF: 0.0896 AC: 1317 AN: 14706

Middle Eastern (MID) AF: 0.161 AC: 192 AN: 1194

European-Non Finnish (NFE) AF: 0.112 AC: 19301 AN: 172468

Other (OTH) AF: 0.154 AC: 2507 AN: 16246

GnomAD4 genome AF: 0.223 AC: 33875 AN: 152160 Hom.: 5354 Cov.: 32 AF XY: 0.221 AC XY: 16427 AN XY: 74410

African (AFR) AF: 0.430 AC: 17851 AN: 41474

American (AMR) AF: 0.339 AC: 5181 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.116 AC: 602 AN: 5178

South Asian (SAS) AF: 0.0920 AC: 444 AN: 4826

European-Finnish (FIN) AF: 0.0801 AC: 850 AN: 10614

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7731 AN: 68000

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.169 Hom.: 4151

Bravo AF: 0.254

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7228082; hg19: chr18-3406933;