dbSNP rs12547643: CASC11:n.144-9062C>T (chr8-127700928-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 ENST00000502463.7(CASC11):n.144-9062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,052 control chromosomes in the GnomAD database, including 6,359 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 0.27 ( 6359 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

CASC11
ENST00000502463.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

13 publications found

Variant links:

Genes affected

CASC11 (HGNC:48939): (cancer susceptibility 11)

CASC11 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 (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC11	NR_117102.1 link	n.560-89C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CASC11	ENST00000502463.7 link	n.144-9062C>T	intron_variant	Intron 1 of 2	2
CASC11	ENST00000519071.6 link	n.549-89C>T	intron_variant	Intron 3 of 3	3
CASC11	ENST00000672637.1 link	n.466-1369C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40658

AN:

151930

Hom.:

6347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.268

AC:

40691

AN:

152048

Hom.:

6359

Cov.:

AF XY:

0.271

AC XY:

20121

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.121

AC:

5012

AN:

41486

American (AMR)

AF:

0.197

AC:

3011

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

1496

AN:

3470

East Asian (EAS)

AF:

0.170

AC:

877

AN:

5174

South Asian (SAS)

AF:

0.453

AC:

2182

AN:

4816

European-Finnish (FIN)

AF:

0.365

AC:

3844

AN:

10538

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23310

AN:

67968

Other (OTH)

AF:

0.283

AC:

598

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1462

2924

4385

5847

7309

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<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:

0.323

Hom.:

16484

Bravo

AF:

0.242

Asia WGS

AF:

0.282

AC:

984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.23

(source)

DANN

Benign

0.36

PhyloP100

-1.2

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