dbSNP rs17077540: DSEL-AS1:n.204+101293A>G (chr18-67618042-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 ENST00000583687.1(DSEL-AS1):n.204+101293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,226 control chromosomes in the GnomAD database, including 861 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 0.10 ( 861 hom., cov: 32)

Consequence

DSEL-AS1
ENST00000583687.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0990

Publications

13 publications found

Variant links:

Genes affected

DSEL-AS1 (HGNC:55325): (DSEL antisense RNA 1)

DSEL-AS1 links:

LOC105372174 (HGNC:):

LOC105372174 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=-0.76).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1 link	n.204+101293A>G		intron_variant	Intron 1 of 4
LOC105372174	XR_935590.3 link	n.105+5746T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1 link	n.204+101293A>G		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15404

AN:

152108

Hom.:

859

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0665

Gnomad AMI

AF:

0.0998

Gnomad AMR

AF:

0.0963

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.0613

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.226

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.130

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

GnomAD4 genome

AF:

0.101

AC:

15407

AN:

152226

Hom.:

861

Cov.:

AF XY:

0.0997

AC XY:

7418

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0662

AC:

2753

AN:

41566

American (AMR)

AF:

0.0962

AC:

1469

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

423

AN:

3470

East Asian (EAS)

AF:

0.115

AC:

594

AN:

5170

South Asian (SAS)

AF:

0.0622

AC:

300

AN:

4826

European-Finnish (FIN)

AF:

0.106

AC:

1120

AN:

10606

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.122

AC:

8316

AN:

67994

Other (OTH)

AF:

0.129

AC:

273

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

703

1406

2108

2811

3514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.118

Hom.:

1749

Bravo

AF:

0.100

Asia WGS

AF:

0.0670

AC:

234

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.9

(source)

DANN

Benign

0.82

PhyloP100

-0.099

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