Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_001229.5(CASP9):c.305C>T(p.Thr102Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,614,176 control chromosomes in the GnomAD database, including 219 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.010 ( 14 hom., cov: 33)

Exomes 𝑓: 0.015 ( 205 hom. )

Consequence

CASP9
NM_001229.5 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.433

Publications

19 publications found

Variant links:

Genes affected

CASP9 (HGNC:1511): (caspase 9) This gene encodes a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic residues to produce two subunits, large and small, that dimerize to form the active enzyme. This protein can undergo autoproteolytic processing and activation by the apoptosome, a protein complex of cytochrome c and the apoptotic peptidase activating factor 1; this step is thought to be one of the earliest in the caspase activation cascade. This protein is thought to play a central role in apoptosis and to be a tumor suppressor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

CASP9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034403205).

BP6

Variant 1-15518223-G-A is Benign according to our data. Variant chr1-15518223-G-A is described in ClinVar as Benign. ClinVar VariationId is 3042052.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0102 (1546/152284) while in subpopulation NFE AF = 0.0166 (1127/68022). AF 95% confidence interval is 0.0158. There are 14 homozygotes in GnomAd4. There are 701 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High AC in GnomAd4 at 1546 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001229.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CASP9	NM_001229.5	MANE Select	c.305C>T	p.Thr102Ile	missense	Exon 2 of 9	NP_001220.2
CASP9	NM_032996.3		c.56C>T	p.Thr19Ile	missense	Exon 2 of 9	NP_127463.2
CASP9	NM_001278054.2		c.305C>T	p.Thr102Ile	missense	Exon 2 of 5	NP_001264983.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CASP9	ENST00000333868.10	TSL:1 MANE Select	c.305C>T	p.Thr102Ile	missense	Exon 2 of 9	ENSP00000330237.5
CASP9	ENST00000348549.9	TSL:1	c.305C>T	p.Thr102Ile	missense	Exon 2 of 5	ENSP00000255256.7
CASP9	ENST00000400777.7	TSL:1	n.296C>T		non_coding_transcript_exon	Exon 2 of 9	ENSP00000383588.3

Frequencies

GnomAD3 genomes

AF:

0.0102

AC:

1546

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00261

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00825

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.0149

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.00766

GnomAD2 exomes

AF:

0.0102

AC:

2572

AN:

251494

AF XY:

0.0101

show subpopulations

Gnomad AFR exome

AF:

0.00215

Gnomad AMR exome

AF:

0.00535

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0147

Gnomad NFE exome

AF:

0.0169

Gnomad OTH exome

AF:

0.0103

GnomAD4 exome

AF:

0.0152

AC:

22254

AN:

1461892

Hom.:

205

Cov.:

AF XY:

0.0147

AC XY:

10655

AN XY:

727246

show subpopulations

African (AFR)

AF:

0.00206

AC:

AN:

33480

American (AMR)

AF:

0.00568

AC:

254

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00142

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00154

AC:

133

AN:

86258

European-Finnish (FIN)

AF:

0.0149

AC:

794

AN:

53420

Middle Eastern (MID)

AF:

0.00121

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0182

AC:

20196

AN:

1112010

Other (OTH)

AF:

0.0126

AC:

764

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

1376

2751

4127

5502

6878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

768

1536

2304

3072

3840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0102

AC:

1546

AN:

152284

Hom.:

Cov.:

AF XY:

0.00941

AC XY:

701

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.00260

AC:

108

AN:

41554

American (AMR)

AF:

0.00824

AC:

126

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.000830

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0149

AC:

158

AN:

10618

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0166

AC:

1127

AN:

68022

Other (OTH)

AF:

0.00758

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

152

227

303

379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0138

Hom.:

Bravo

AF:

0.00915

TwinsUK

AF:

0.0216

AC:

ALSPAC

AF:

0.0189

AC:

ESP6500AA

AF:

0.00386

AC:

ESP6500EA

AF:

0.0145

AC:

125

ExAC

AF:

0.0108

AC:

1312

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0136

EpiControl

AF:

0.0140

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

CASP9-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.4

(source)

DANN

Benign

0.80

DEOGEN2

Benign

0.12

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.99

FATHMM_MKL

Benign

0.093

LIST_S2

Benign

0.64

MetaRNN

Benign

0.0034

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.0

PhyloP100

0.43

PrimateAI

Benign

0.31

PROVEAN

Benign

-1.1

REVEL

Benign

0.045

Sift

Benign

0.12

Sift4G

Benign

0.20

Polyphen

0.70

Vest4

0.039

MPC

0.13

ClinPred

0.0081

GERP RS

-1.2

Varity_R

0.053

gMVP

0.26

Mutation Taster

=95/5

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs2308941

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over