Genetic Variant ENST00000483840.1:n.106-14251C>T (chr3-101980310-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Publications

7 publications found

Variant links:

Genes affected

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

RDUR links:

Genome browser will be placed here

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=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDUR	NR_026934.1 link	n.269-14251C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
RDUR	ENST00000483840.1 link	n.106-14251C>T	intron_variant	Intron 1 of 2	1
RDUR	ENST00000498624.1 link	n.347-14251C>T	intron_variant	Intron 1 of 2	1
RDUR	ENST00000465215.1 link	n.269-14251C>T	intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.544

AC:

82627

AN:

151918

Hom.:

22864

Cov.:

show subpopulations

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.:

AF XY:

0.539

AC XY:

40065

AN XY:

74320

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1926

3852

5778

7704

9630

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.575

Hom.:

11979

Bravo

AF:

0.542

Asia WGS

AF:

0.499

AC:

1737

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.12

(source)

DANN

Benign

0.66

PhyloP100

-1.4

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