rs2020903

Positions:

• chr1-15507802-G-A
• chr1-15507802-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001229.5(CASP9):​c.453+71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 1,485,308 control chromosomes in the GnomAD database, including 218,191 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 0.59 (26824 hom., cov: 32)
  • Exomes 𝑓: 0.53 (191367 hom.)
• Consequence: CASP9 NM_001229.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASP9	NM_001229.5	c.453+71C>T		intron_variant		ENST00000333868.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASP9	ENST00000333868.10	c.453+71C>T		intron_variant		1	NM_001229.5	P1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89086 AN: 151912 Hom.: 26783 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.532 AC: 709049 AN: 1333276 Hom.: 191367 Cov.: 19 AF XY: 0.529 AC XY: 354294 AN XY: 669712

Gnomad4 AFR exome AF: 0.703

Gnomad4 AMR exome AF: 0.418

Gnomad4 ASJ exome AF: 0.492

Gnomad4 EAS exome AF: 0.644

Gnomad4 SAS exome AF: 0.432

Gnomad4 FIN exome AF: 0.638

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.539

GnomAD4 genome AF: 0.587 AC: 89176 AN: 152032 Hom.: 26824 Cov.: 32 AF XY: 0.587 AC XY: 43642 AN XY: 74324

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.552

Alfa AF: 0.563 Hom.: 3061

Bravo AF: 0.581

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.7
DANN	Benign	0.62

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

LitVar

Other links and lift over

dbSNP: rs2020903; hg19: chr1-15834297; COSMIC: COSV61601098; COSMIC: COSV61601098;