dbSNP rs7170930: DIS3L-AS1:n.167+4811G>A (chr15-66288515-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000564269.2(DIS3L-AS1):n.167+4811G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,254 control chromosomes in the GnomAD database, including 391 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 0.065 ( 391 hom., cov: 32)

Consequence

DIS3L-AS1
ENST00000564269.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164

Publications

14 publications found

Variant links:

COSMIC-nc: COSV59913531

Genes affected

DIS3L-AS1 (HGNC:55369): (DIS3L antisense RNA 1)

DIS3L-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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.08 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
DIS3L-AS1	NR_183865.1 link	n.275-2328G>A	intron_variant	Intron 1 of 1
DIS3L-AS1	NR_183866.1 link	n.274+4711G>A	intron_variant	Intron 1 of 1
DIS3L-AS1	NR_183867.1 link	n.174+4811G>A	intron_variant	Intron 1 of 1
DIS3L-AS1	NR_183868.1 link	n.175-2328G>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIS3L-AS1	ENST00000564269.2 link	n.167+4811G>A		intron_variant	Intron 1 of 1	2
DIS3L-AS1	ENST00000784663.1 link	n.265+4711G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0651

AC:

9906

AN:

152136

Hom.:

390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0460

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0555

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.00269

Gnomad SAS

AF:

0.0339

Gnomad FIN

AF:

0.0694

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0818

Gnomad OTH

AF:

0.0756

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

GnomAD4 genome

AF:

0.0651

AC:

9910

AN:

152254

Hom.:

391

Cov.:

AF XY:

0.0633

AC XY:

4710

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0460

AC:

1910

AN:

41560

American (AMR)

AF:

0.0555

AC:

848

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

410

AN:

3468

East Asian (EAS)

AF:

0.00270

AC:

AN:

5190

South Asian (SAS)

AF:

0.0346

AC:

167

AN:

4830

European-Finnish (FIN)

AF:

0.0694

AC:

734

AN:

10580

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0818

AC:

5567

AN:

68018

Other (OTH)

AF:

0.0748

AC:

158

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

468

936

1404

1872

2340

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0596

Hom.:

119

Bravo

AF:

0.0634

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.7

(source)

DANN

Benign

0.61

PhyloP100

0.16

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