dbSNP rs4871799: CASC8:n.1041+8686C>T (chr8-127470397-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+8686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,172 control chromosomes in the GnomAD database, including 37,869 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 0.70 ( 37869 hom., cov: 32)

Consequence

CASC8
ENST00000502056.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

Publications

8 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC8	NR_024393.1 link	n.1041+8686C>T		intron_variant	Intron 4 of 4
CASC8	NR_117100.1 link	n.1041+8686C>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+8686C>T		intron_variant	Intron 4 of 4	1
CASC8	ENST00000502082.5 link	n.1041+8686C>T		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.700

AC:

106491

AN:

152054

Hom.:

37873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.782

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.773

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.766

Gnomad OTH

AF:

0.721

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

GnomAD4 genome

AF:

0.700

AC:

106519

AN:

152172

Hom.:

37869

Cov.:

AF XY:

0.698

AC XY:

51914

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.574

AC:

23828

AN:

41512

American (AMR)

AF:

0.736

AC:

11261

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.782

AC:

2715

AN:

3472

East Asian (EAS)

AF:

0.630

AC:

3256

AN:

5170

South Asian (SAS)

AF:

0.774

AC:

3732

AN:

4824

European-Finnish (FIN)

AF:

0.676

AC:

7143

AN:

10574

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.766

AC:

52095

AN:

68008

Other (OTH)

AF:

0.716

AC:

1513

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1592

3183

4775

6366

7958

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.745

Hom.:

131274

Bravo

AF:

0.697

Asia WGS

AF:

0.657

AC:

2288

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.45

(source)

DANN

Benign

0.94

PhyloP100

-1.7

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