Genetic Variant DICER1-AS1:n.385-5512C>A (chr14-95173992-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000435343.2(DICER1-AS1):n.385-5512C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,296 control chromosomes in the GnomAD database, including 423 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 0.066 ( 423 hom., cov: 32)

Consequence

DICER1-AS1
ENST00000435343.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Publications

2 publications found

Variant links:

Genes affected

DICER1-AS1 (HGNC:43017): (DICER1 antisense RNA 1)

DICER1-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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DICER1-AS1	NR_015415.1 link	n.374-5512C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DICER1-AS1	ENST00000435343.2 link	n.385-5512C>A	intron_variant	Intron 3 of 3	3
DICER1-AS1	ENST00000439819.8 link	n.404-5507C>A	intron_variant	Intron 3 of 3	3
DICER1-AS1	ENST00000554631.2 link	n.1392-5507C>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0662

AC:

10076

AN:

152178

Hom.:

420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.0396

Gnomad ASJ

AF:

0.0764

Gnomad EAS

AF:

0.000576

Gnomad SAS

AF:

0.0153

Gnomad FIN

AF:

0.0457

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.0526

Gnomad OTH

AF:

0.0636

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

GnomAD4 genome

AF:

0.0663

AC:

10093

AN:

152296

Hom.:

423

Cov.:

AF XY:

0.0645

AC XY:

4805

AN XY:

74484

show subpopulations

African (AFR)

AF:

0.116

AC:

4818

AN:

41556

American (AMR)

AF:

0.0395

AC:

605

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0764

AC:

265

AN:

3468

East Asian (EAS)

AF:

0.000578

AC:

AN:

5192

South Asian (SAS)

AF:

0.0153

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0457

AC:

485

AN:

10608

Middle Eastern (MID)

AF:

0.0993

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0526

AC:

3579

AN:

68020

Other (OTH)

AF:

0.0624

AC:

132

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

488

976

1464

1952

2440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0618

Hom.:

664

Bravo

AF:

0.0685

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.5

(source)

DANN

Benign

0.44

PhyloP100

0.26

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