dbSNP rs7012462: CASC8:n.1042-1725A>G (chr8-127445445-T-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.1042-1725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,150 control chromosomes in the GnomAD database, including 30,313 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 0.63 ( 30313 hom., cov: 34)

Consequence

CASC8
ENST00000502056.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.764

Publications

7 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC8	NR_024393.1 link	n.1042-1725A>G		intron_variant	Intron 4 of 4
CASC8	NR_117100.1 link	n.1042-24482A>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.1042-1725A>G		intron_variant	Intron 4 of 4	1
CASC8	ENST00000502082.5 link	n.1042-24482A>G		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.628

AC:

95541

AN:

152032

Hom.:

30279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.716

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.606

Gnomad ASJ

AF:

0.637

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.589

Gnomad OTH

AF:

0.607

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

GnomAD4 genome

AF:

0.628

AC:

95622

AN:

152150

Hom.:

30313

Cov.:

AF XY:

0.624

AC XY:

46441

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.716

AC:

29692

AN:

41492

American (AMR)

AF:

0.606

AC:

9265

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.637

AC:

2209

AN:

3468

East Asian (EAS)

AF:

0.662

AC:

3423

AN:

5172

South Asian (SAS)

AF:

0.554

AC:

2671

AN:

4824

European-Finnish (FIN)

AF:

0.593

AC:

6289

AN:

10598

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.589

AC:

40056

AN:

67984

Other (OTH)

AF:

0.612

AC:

1292

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1842

3684

5525

7367

9209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.603

Hom.:

34650

Bravo

AF:

0.632

Asia WGS

AF:

0.623

AC:

2167

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.10

(source)

DANN

Benign

0.38

PhyloP100

-0.76

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