rs17842780

Variant names:

• chr3-101888320-A-G
• rs17842780
• ENST00000657494.1:n.226+1488A>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+1488A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,132 control chromosomes in the GnomAD database, including 5,170 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 0.26 (5170 hom., cov: 32)
• Consequence: RDUR ENST00000657494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 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
RDUR	ENST00000657494.1	n.226+1488A>G		intron_variant	Intron 2 of 3
RDUR	ENST00000772038.1	n.205+1488A>G		intron_variant	Intron 2 of 3
RDUR	ENST00000772039.1	n.230+1488A>G		intron_variant	Intron 2 of 3
RDUR	ENST00000772040.1	n.258+1488A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38752 AN: 152014 Hom.: 5158 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0939

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.255 AC: 38802 AN: 152132 Hom.: 5170 Cov.: 32 AF XY: 0.256 AC XY: 19040 AN XY: 74350

African (AFR) AF: 0.245 AC: 10150 AN: 41500

American (AMR) AF: 0.341 AC: 5210 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.0941 AC: 488 AN: 5184

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2988 AN: 10580

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17293 AN: 67980

Other (OTH) AF: 0.264 AC: 558 AN: 2116

Alfa AF: 0.254 Hom.: 21264

Bravo AF: 0.260

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17842780; hg19: chr3-101607164; COSMIC: COSV53460789;