dbSNP rs4730250: DUS4L:c.116+64A>G (chr7-107567250-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 NM_181581.3(DUS4L):c.116+64A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,432,380 control chromosomes in the GnomAD database, including 19,894 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 0.12 ( 1477 hom., cov: 32)

Exomes 𝑓: 0.17 ( 18417 hom. )

Consequence

DUS4L
NM_181581.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291

Publications

43 publications found

Variant links:

Genes affected

DUS4L (HGNC:21517): (dihydrouridine synthase 4 like) Predicted to enable tRNA dihydrouridine synthase activity. Predicted to be involved in tRNA dihydrouridine synthesis. [provided by Alliance of Genome Resources, Apr 2022]

DUS4L links:

DUS4L-BCAP29 (HGNC:54422): (DUS4L-BCAP29 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring DUS4L (dihydrouridine synthase 4 like) and BCAP29 (B cell receptor associated protein 29) genes on chromosome 7. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2019]

DUS4L-BCAP29 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUS4L	NM_181581.3 link	c.116+64A>G		intron_variant	Intron 3 of 7	ENST00000265720.8	NP_853559.1	O95620-1A4D0R5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUS4L	ENST00000265720.8 link	c.116+64A>G		intron_variant	Intron 3 of 7	2	NM_181581.3	ENSP00000265720.3		O95620-1
DUS4L-BCAP29	ENST00000673665.1 link	c.116+64A>G		intron_variant	Intron 2 of 12			ENSP00000501082.1		A0A669KB27

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18921

AN:

152074

Hom.:

1479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0335

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.124

GnomAD4 exome

AF:

0.168

AC:

214648

AN:

1280188

Hom.:

18417

AF XY:

0.167

AC XY:

107113

AN XY:

641860

show subpopulations

African (AFR)

AF:

0.0276

AC:

786

AN:

28434

American (AMR)

AF:

0.141

AC:

5482

AN:

38756

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

3988

AN:

24044

East Asian (EAS)

AF:

0.116

AC:

4259

AN:

36812

South Asian (SAS)

AF:

0.140

AC:

10895

AN:

78036

European-Finnish (FIN)

AF:

0.157

AC:

7926

AN:

50610

Middle Eastern (MID)

AF:

0.112

AC:

601

AN:

5366

European-Non Finnish (NFE)

AF:

0.179

AC:

172552

AN:

964210

Other (OTH)

AF:

0.151

AC:

8159

AN:

53920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

8467

16934

25402

33869

42336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5926

11852

17778

23704

29630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.124

AC:

18915

AN:

152192

Hom.:

1477

Cov.:

AF XY:

0.123

AC XY:

9160

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0334

AC:

1387

AN:

41562

American (AMR)

AF:

0.131

AC:

2004

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

548

AN:

3470

East Asian (EAS)

AF:

0.135

AC:

699

AN:

5176

South Asian (SAS)

AF:

0.135

AC:

653

AN:

4828

European-Finnish (FIN)

AF:

0.152

AC:

1615

AN:

10592

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11512

AN:

67952

Other (OTH)

AF:

0.124

AC:

262

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

825

1651

2476

3302

4127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.152

Hom.:

3866

Bravo

AF:

0.121

Asia WGS

AF:

0.147

AC:

512

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.3

(source)

DANN

Benign

0.64

PhyloP100

0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over