Genetic Variant DSEL-AS1:n.205-16367G>A (chr18-67818052-G-A) – 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.205-16367G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,844 control chromosomes in the GnomAD database, including 31,962 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 0.61 ( 31962 hom., cov: 33)

Consequence

DSEL-AS1
ENST00000583687.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.362

Publications

1 publications found

Variant links:

Genes affected

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

DSEL-AS1 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1 link	n.205-16367G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1 link	n.205-16367G>A		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93282

AN:

151726

Hom.:

31959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.697

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.552

Gnomad EAS

AF:

0.919

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.866

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.611

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

GnomAD4 genome

AF:

0.614

AC:

93299

AN:

151844

Hom.:

31962

Cov.:

AF XY:

0.629

AC XY:

46665

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.302

AC:

12501

AN:

41438

American (AMR)

AF:

0.718

AC:

10948

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.552

AC:

1916

AN:

3470

East Asian (EAS)

AF:

0.920

AC:

4757

AN:

5172

South Asian (SAS)

AF:

0.766

AC:

3696

AN:

4828

European-Finnish (FIN)

AF:

0.866

AC:

9179

AN:

10596

Middle Eastern (MID)

AF:

0.592

AC:

174

AN:

294

European-Non Finnish (NFE)

AF:

0.711

AC:

48210

AN:

67774

Other (OTH)

AF:

0.609

AC:

1282

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1545

3090

4635

6180

7725

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

750

1500

2250

3000

3750

<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:

0.682

Hom.:

15100

Bravo

AF:

0.592

Asia WGS

AF:

0.809

AC:

2809

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.8

(source)

DANN

Benign

0.53

PhyloP100

-0.36

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