Genetic Variant RDUR:n.226+15006A>G (chr3-101901838-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

5 publications found

Variant links:

Genes affected

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

RDUR links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
RDUR	ENST00000657494.1 link	n.226+15006A>G	intron_variant	Intron 2 of 3
RDUR	ENST00000772038.1 link	n.205+15006A>G	intron_variant	Intron 2 of 3
RDUR	ENST00000772039.1 link	n.335+2552A>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42347

AN:

151864

Hom.:

6284

Cov.:

show subpopulations

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.:

AF XY:

0.275

AC XY:

20407

AN XY:

74290

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.326

AC:

22138

AN:

67934

Other (OTH)

AF:

0.269

AC:

569

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1562

3123

4685

6246

7808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.2

(source)

DANN

Benign

0.76

PhyloP100

0.16

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over