Genetic Variant CASC9:n.89+6499C>A (chr8-75318066-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000521147.2(CASC9):n.89+6499C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,136 control chromosomes in the GnomAD database, including 56,526 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 0.86 ( 56526 hom., cov: 33)

Consequence

CASC9
ENST00000521147.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370

Publications

65 publications found

Variant links:

Genes affected

CASC9 (HGNC:48906): (cancer susceptibility 9)

CASC9 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 = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CASC9	ENST00000521147.2 link	n.89+6499C>A	intron_variant	Intron 1 of 2	2
CASC9	ENST00000654852.3 link	n.177+6499C>A	intron_variant	Intron 1 of 1
CASC9	ENST00000669950.2 link	n.500+6155C>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.861

AC:

130937

AN:

152018

Hom.:

56471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.900

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.896

Gnomad ASJ

AF:

0.829

Gnomad EAS

AF:

0.964

Gnomad SAS

AF:

0.898

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.937

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.873

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

GnomAD4 genome

AF:

0.861

AC:

131053

AN:

152136

Hom.:

56526

Cov.:

AF XY:

0.865

AC XY:

64300

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.900

AC:

37401

AN:

41534

American (AMR)

AF:

0.896

AC:

13691

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.829

AC:

2879

AN:

3472

East Asian (EAS)

AF:

0.964

AC:

4996

AN:

5184

South Asian (SAS)

AF:

0.898

AC:

4334

AN:

4826

European-Finnish (FIN)

AF:

0.809

AC:

8567

AN:

10592

Middle Eastern (MID)

AF:

0.935

AC:

275

AN:

294

European-Non Finnish (NFE)

AF:

0.829

AC:

56353

AN:

67942

Other (OTH)

AF:

0.876

AC:

1846

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

945

1891

2836

3782

4727

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<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:

0.844

Hom.:

168315

Bravo

AF:

0.869

Asia WGS

AF:

0.939

AC:

3265

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

0.94

(source)

DANN

Benign

0.38

PhyloP100

-0.037

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