dbSNP rs16902364: CASC11:n.143+805T>G (chr8-127733020-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 ENST00000502463.7(CASC11):n.143+805T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,038 control chromosomes in the GnomAD database, including 2,451 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 0.13 ( 2451 hom., cov: 32)

Consequence

CASC11
ENST00000502463.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.944

Publications

9 publications found

Variant links:

COSMIC-nc: COSV104583426

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC11	NR_117101.1 link	n.143+805T>G		intron_variant	Intron 1 of 1
CASC11	NR_117102.1 link	n.143+805T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CASC11	ENST00000502463.7 link	n.143+805T>G	intron_variant	Intron 1 of 2	2
CASC11	ENST00000518376.2 link	n.141+805T>G	intron_variant	Intron 1 of 1	3
CASC11	ENST00000519071.6 link	n.132+805T>G	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20004

AN:

151920

Hom.:

2438

Cov.:

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.0925

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0342

Gnomad OTH

AF:

0.0877

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

GnomAD4 genome

AF:

0.132

AC:

20061

AN:

152038

Hom.:

2451

Cov.:

AF XY:

0.135

AC XY:

10051

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.312

AC:

12942

AN:

41418

American (AMR)

AF:

0.107

AC:

1639

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0389

AC:

135

AN:

3466

East Asian (EAS)

AF:

0.210

AC:

1085

AN:

5174

South Asian (SAS)

AF:

0.153

AC:

736

AN:

4814

European-Finnish (FIN)

AF:

0.0925

AC:

981

AN:

10602

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0342

AC:

2328

AN:

67974

Other (OTH)

AF:

0.0873

AC:

184

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

784

1569

2353

3138

3922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.0647

Hom.:

2862

Bravo

AF:

0.135

Asia WGS

AF:

0.161

AC:

562

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

1.1

(source)

DANN

Benign

0.72

PhyloP100

-0.94

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