rs10511192

Variant names:

• chr3-101994788-C-T
• rs10511192
• ENST00000483840.1:n.333C>T

Variant summary

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

The ENST00000483840.1(ENSG00000241280):​n.333C>T 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 0.303 in 152,442 control chromosomes in the GnomAD database, including 7,198 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 0.30 (7188 hom., cov: 32)
  • Exomes 𝑓: 0.26 (10 hom.)
• Consequence: ENSG00000241280 ENST00000483840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

ENSG00000241280 (HGNC:):

RDUR (HGNC:27190): (RIG-I dependent antiviral response regulator RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDUR	NR_026934.1	n.496C>T		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000241280	ENST00000483840.1	n.333C>T		non_coding_transcript_exon_variant	Exon 2 of 3	1
ENSG00000241280	ENST00000498624.1	n.454+120C>T		intron_variant	Intron 2 of 2	1
RDUR	ENST00000465215.1	n.496C>T		non_coding_transcript_exon_variant	Exon 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46006 AN: 151862 Hom.: 7182 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.260 AC: 120 AN: 462 Hom.: 10 Cov.: 0 AF XY: 0.265 AC XY: 72 AN XY: 272

Gnomad4 FIN exome AF: 0.256

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.303 AC: 46037 AN: 151980 Hom.: 7188 Cov.: 32 AF XY: 0.297 AC XY: 22092 AN XY: 74284

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.339

Alfa AF: 0.329 Hom.: 2991

Bravo AF: 0.309

Asia WGS AF: 0.312 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.85
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511192; hg19: chr3-101713632;