Genetic Variant ENST00000560323.1:n.303A>G (chr15-48314955-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000560323.1(DUT-AS1):n.303A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,302 control chromosomes in the GnomAD database, including 3,066 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 0.19 ( 3065 hom., cov: 33)

Exomes 𝑓: 0.19 ( 1 hom. )

Consequence

DUT-AS1
ENST00000560323.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

11 publications found

Variant links:

Genes affected

DUT-AS1 (HGNC:55420): (DUT antisense RNA 1)

DUT-AS1 links:

ENSG00000303148 (HGNC:):

ENSG00000303148 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUT-AS1	NR_186809.1 link	n.303A>G		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUT-AS1	ENST00000560323.1 link	n.303A>G		non_coding_transcript_exon_variant	Exon 2 of 3	3
ENSG00000303148	ENST00000792186.1 link	n.189+1275T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29343

AN:

152146

Hom.:

3060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.209

GnomAD4 exome

AF:

0.194

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.133

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.193

AC:

29382

AN:

152266

Hom.:

3065

Cov.:

AF XY:

0.190

AC XY:

14187

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.268

AC:

11142

AN:

41534

American (AMR)

AF:

0.196

AC:

3004

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

663

AN:

3472

East Asian (EAS)

AF:

0.190

AC:

984

AN:

5184

South Asian (SAS)

AF:

0.212

AC:

1025

AN:

4832

European-Finnish (FIN)

AF:

0.132

AC:

1406

AN:

10612

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.156

AC:

10600

AN:

68018

Other (OTH)

AF:

0.214

AC:

451

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1209

2419

3628

4838

6047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.174

Hom.:

615

Bravo

AF:

0.201

Asia WGS

AF:

0.227

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.0

(source)

DANN

Benign

0.80

PhyloP100

1.0

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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