ENST00000657494.1:n.226+15006A>G

Variant names:

• chr3-101901838-A-G
• rs771574
• ENST00000657494.1:n.226+15006A>G

Variant summary

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

The ENST00000657494.1(RDUR):​n.226+15006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,982 control chromosomes in the GnomAD database, including 6,282 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 0.28 (6282 hom., cov: 32)
• Consequence: RDUR ENST00000657494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657494.1. 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
	RDUR	ENST00000657494.1		n.226+15006A>G		intron	N/A
	RDUR	ENST00000772038.1		n.205+15006A>G		intron	N/A
	RDUR	ENST00000772039.1		n.335+2552A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42347 AN: 151864 Hom.: 6284 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.279 AC: 42368 AN: 151982 Hom.: 6282 Cov.: 32 AF XY: 0.275 AC XY: 20407 AN XY: 74290

African (AFR) AF: 0.202 AC: 8394 AN: 41478

American (AMR) AF: 0.219 AC: 3336 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3468

East Asian (EAS) AF: 0.452 AC: 2328 AN: 5150

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4810

European-Finnish (FIN) AF: 0.256 AC: 2709 AN: 10564

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22138 AN: 67934

Other (OTH) AF: 0.269 AC: 569 AN: 2114

Alfa AF: 0.307 Hom.: 20593

Bravo AF: 0.278

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.76
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs771574; hg19: chr3-101620682;