Genetic Variant CASC6:n.717+19838A>C (chr6-91604261-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000656997.1(CASC6):n.717+19838A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,082 control chromosomes in the GnomAD database, including 10,784 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 0.36 ( 10784 hom., cov: 33)

Consequence

CASC6
ENST00000656997.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

2 publications found

Variant links:

COSMIC-nc: COSV60245798

Genes affected

CASC6 (HGNC:49076): (cancer susceptibility 6)

CASC6 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CASC6	ENST00000656997.1 link	n.717+19838A>C	intron_variant	Intron 2 of 3
CASC6	ENST00000760409.1 link	n.564+19838A>C	intron_variant	Intron 2 of 3
CASC6	ENST00000760410.1 link	n.388+19838A>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55433

AN:

151964

Hom.:

10786

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.706

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.450

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.336

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

GnomAD4 genome

AF:

0.365

AC:

55438

AN:

152082

Hom.:

10784

Cov.:

AF XY:

0.376

AC XY:

27965

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.283

AC:

11753

AN:

41486

American (AMR)

AF:

0.439

AC:

6705

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1021

AN:

3472

East Asian (EAS)

AF:

0.706

AC:

3628

AN:

5142

South Asian (SAS)

AF:

0.486

AC:

2343

AN:

4824

European-Finnish (FIN)

AF:

0.450

AC:

4770

AN:

10596

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.356

AC:

24197

AN:

67974

Other (OTH)

AF:

0.334

AC:

706

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1793

3585

5378

7170

8963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

554

1108

1662

2216

2770

<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:

0.360

Hom.:

42935

Bravo

AF:

0.362

Asia WGS

AF:

0.526

AC:

1825

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.97

(source)

DANN

Benign

0.60

PhyloP100

0.31

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