Genetic Variant ENST00000722184.1:n.297-21069A>G (chr20-6547561-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 ENST00000722184.1(CASC20):n.297-21069A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,820 control chromosomes in the GnomAD database, including 1,288 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 0.12 ( 1288 hom., cov: 32)

Consequence

CASC20
ENST00000722184.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.833

Publications

1 publications found

Variant links:

Genes affected

CASC20 (HGNC:49477): (cancer susceptibility 20)

CASC20 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CASC20	ENST00000722184.1 link	n.297-21069A>G	intron_variant	Intron 1 of 2
CASC20	ENST00000722185.1 link	n.280-21069A>G	intron_variant	Intron 2 of 3
CASC20	ENST00000722186.1 link	n.477+12817A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18503

AN:

151700

Hom.:

1283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.00757

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.0448

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.149

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

GnomAD4 genome

AF:

0.122

AC:

18516

AN:

151820

Hom.:

1288

Cov.:

AF XY:

0.117

AC XY:

8714

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.154

AC:

6363

AN:

41422

American (AMR)

AF:

0.106

AC:

1609

AN:

15202

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

882

AN:

3460

East Asian (EAS)

AF:

0.00740

AC:

AN:

5138

South Asian (SAS)

AF:

0.112

AC:

541

AN:

4810

European-Finnish (FIN)

AF:

0.0448

AC:

475

AN:

10604

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8181

AN:

67870

Other (OTH)

AF:

0.148

AC:

311

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

824

1648

2472

3296

4120

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.115

Hom.:

150

Bravo

AF:

0.127

Asia WGS

AF:

0.0790

AC:

275

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.41

PhyloP100

-0.83

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