dbSNP rs7825118: CASC8:n.1041+15511C>T (chr8-127463572-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000502056.1(CASC8):n.1041+15511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,130 control chromosomes in the GnomAD database, including 3,741 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 0.20 ( 3741 hom., cov: 31)

Consequence

CASC8
ENST00000502056.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.205

Publications

3 publications found

Variant links:

Genes affected

CASC8 (HGNC:45129): (cancer susceptibility 8)

CASC8 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 (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC8	NR_024393.1 link	n.1041+15511C>T		intron_variant	Intron 4 of 4
CASC8	NR_117100.1 link	n.1041+15511C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC8	ENST00000502056.1 link	n.1041+15511C>T		intron_variant	Intron 4 of 4	1
CASC8	ENST00000502082.5 link	n.1041+15511C>T		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31176

AN:

152014

Hom.:

3742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0866

Gnomad AMI

AF:

0.425

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.205

AC:

31170

AN:

152130

Hom.:

3741

Cov.:

AF XY:

0.208

AC XY:

15439

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.0864

AC:

3589

AN:

41550

American (AMR)

AF:

0.285

AC:

4357

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

933

AN:

3470

East Asian (EAS)

AF:

0.230

AC:

1189

AN:

5160

South Asian (SAS)

AF:

0.221

AC:

1066

AN:

4818

European-Finnish (FIN)

AF:

0.267

AC:

2812

AN:

10536

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16280

AN:

67994

Other (OTH)

AF:

0.223

AC:

471

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1233

2465

3698

4930

6163

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.221

Hom.:

6952

Bravo

AF:

0.206

Asia WGS

AF:

0.216

AC:

749

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

6.6

(source)

DANN

Benign

0.59

PhyloP100

0.20

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