rs1709393

Variant names:

• chr3-101980310-C-T
• rs1709393
• ENST00000483840.1:n.106-14251C>T

Variant summary

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

The ENST00000483840.1(RDUR):​n.106-14251C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,036 control chromosomes in the GnomAD database, including 22,897 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 0.54 (22897 hom., cov: 33)
• Consequence: RDUR ENST00000483840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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.269-14251C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RDUR	ENST00000483840.1	TSL:1	n.106-14251C>T		intron	N/A
	RDUR	ENST00000498624.1	TSL:1	n.347-14251C>T		intron	N/A
	RDUR	ENST00000465215.1	TSL:2	n.269-14251C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82627 AN: 151918 Hom.: 22864 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.544 AC: 82721 AN: 152036 Hom.: 22897 Cov.: 33 AF XY: 0.539 AC XY: 40065 AN XY: 74320

African (AFR) AF: 0.510 AC: 21140 AN: 41474

American (AMR) AF: 0.521 AC: 7950 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2231 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1994 AN: 5172

South Asian (SAS) AF: 0.574 AC: 2770 AN: 4822

European-Finnish (FIN) AF: 0.477 AC: 5032 AN: 10550

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39739 AN: 67964

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.575 Hom.: 11979

Bravo AF: 0.542

Asia WGS AF: 0.499 AC: 1737 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1709393;

hg19: chr3-101699154;