rs11881682

Variant names:

• chr19-7750490-G-A
• rs11881682
• ENST00000491732.1:n.-194G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-7750490-G-A
• chr19-7750490-G-C

Variant summary

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

The ENST00000491732.1(RPL21P129):​n.-194G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,080 control chromosomes in the GnomAD database, including 2,368 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 0.17 (2368 hom., cov: 31)
• Consequence: RPL21P129 ENST00000491732.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

RPL21P129 (HGNC:36747): (ribosomal protein L21 pseudogene 129)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL21P129	ENST00000491732.1	n.-194G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26283 AN: 151962 Hom.: 2365 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0635

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.173 AC: 26291 AN: 152080 Hom.: 2368 Cov.: 31 AF XY: 0.173 AC XY: 12864 AN XY: 74374

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0634

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.154

Alfa AF: 0.164 Hom.: 2082

Bravo AF: 0.172

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11881682; hg19: chr19-7815376;