Genetic Variant ENST00000722184.1:n.297-39397A>C (chr20-6529233-A-C) – 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.297-39397A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,172 control chromosomes in the GnomAD database, including 2,449 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 0.16 ( 2449 hom., cov: 32)

Consequence

CASC20
ENST00000722184.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.56

Publications

4 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC20	ENST00000722184.1 link	n.297-39397A>C		intron_variant	Intron 1 of 2
CASC20	ENST00000722185.1 link	n.280-39397A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23655

AN:

152054

Hom.:

2431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.00750

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0431

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.156

AC:

23713

AN:

152172

Hom.:

2449

Cov.:

AF XY:

0.151

AC XY:

11215

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.278

AC:

11533

AN:

41466

American (AMR)

AF:

0.120

AC:

1828

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

883

AN:

3468

East Asian (EAS)

AF:

0.00732

AC:

AN:

5190

South Asian (SAS)

AF:

0.115

AC:

557

AN:

4824

European-Finnish (FIN)

AF:

0.0431

AC:

457

AN:

10614

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7925

AN:

68012

Other (OTH)

AF:

0.176

AC:

373

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

960

1920

2880

3840

4800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.130

Hom.:

883

Bravo

AF:

0.165

Asia WGS

AF:

0.0890

AC:

312

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

8.2

(source)

DANN

Benign

0.65

PhyloP100

1.6

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