chr3-101994788-C-T

Variant names:

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

Variant summary

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

The ENST00000483840.1(RDUR):​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: RDUR ENST00000483840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000483840.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RDUR	NR_026934.1		n.496C>T		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RDUR	ENST00000483840.1	TSL:1	n.333C>T		non_coding_transcript_exon	Exon 2 of 3
	RDUR	ENST00000498624.1	TSL:1	n.454+120C>T		intron	N/A
	RDUR	ENST00000465215.1	TSL:2	n.496C>T		non_coding_transcript_exon	Exon 3 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.256 AC: 111 AN: 434

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.188 AC: 3 AN: 16

Other (OTH) AF: 0.500 AC: 6 AN: 12

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

African (AFR) AF: 0.263 AC: 10925 AN: 41470

American (AMR) AF: 0.286 AC: 4355 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5166

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4818

European-Finnish (FIN) AF: 0.229 AC: 2423 AN: 10568

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22701 AN: 67932

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.327 Hom.: 4815

Bravo AF: 0.309

Asia WGS AF: 0.312 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.85
DANN	Benign	0.62
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10511192; hg19: chr3-101713632;