dbSNP rs6470519: CASC8:n.1041+7105T>G (chr8-127471978-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 ENST00000502056.1(CASC8):n.1041+7105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,098 control chromosomes in the GnomAD database, including 57,930 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 0.87 ( 57930 hom., cov: 31)

Consequence

CASC8
ENST00000502056.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.195

Publications

9 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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC8	NR_024393.1 link	n.1041+7105T>G		intron_variant	Intron 4 of 4
CASC8	NR_117100.1 link	n.1041+7105T>G		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+7105T>G		intron_variant	Intron 4 of 4	1
CASC8	ENST00000502082.5 link	n.1041+7105T>G		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.872

AC:

132459

AN:

151982

Hom.:

57897

Cov.:

show subpopulations

Gnomad AFR

AF:

0.817

Gnomad AMI

AF:

0.904

Gnomad AMR

AF:

0.913

Gnomad ASJ

AF:

0.940

Gnomad EAS

AF:

0.851

Gnomad SAS

AF:

0.872

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.899

Gnomad OTH

AF:

0.888

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

GnomAD4 genome

AF:

0.871

AC:

132543

AN:

152098

Hom.:

57930

Cov.:

AF XY:

0.869

AC XY:

64574

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.817

AC:

33873

AN:

41456

American (AMR)

AF:

0.912

AC:

13954

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.940

AC:

3263

AN:

3470

East Asian (EAS)

AF:

0.851

AC:

4403

AN:

5176

South Asian (SAS)

AF:

0.873

AC:

4207

AN:

4818

European-Finnish (FIN)

AF:

0.825

AC:

8716

AN:

10566

Middle Eastern (MID)

AF:

0.959

AC:

282

AN:

294

European-Non Finnish (NFE)

AF:

0.899

AC:

61152

AN:

67994

Other (OTH)

AF:

0.883

AC:

1869

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

840

1680

2520

3360

4200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

896

1792

2688

3584

4480

<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:

0.896

Hom.:

95585

Bravo

AF:

0.873

Asia WGS

AF:

0.809

AC:

2814

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

5.4

(source)

DANN

Benign

0.60

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