rs4645982

Variant names:

• chr1-15524569-ATCCCCGCACTGACCTCACG-A
• rs4645982
• NM_032996.3:c.-123_-118+13delCGTGAGGTCAGTGCGGGGA

Your query was ambiguous. Multiple possible variants found:

• chr1-15524569-ATCCCCGCACTGACCTCACG-A
• chr1-15524569-ATCCCCGCACTGACCTCACG-ATCCCCGCACTGACCTCACGTCCCCGCACTGACCTCACG
• chr1-15524569-ATCCCCGCACTGACCTCACG-ATCCCCGCACTGACCTCACGTCCCCGCACTGACCTCACGTCCCCGCACTGACCTCACG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_032996.3(CASP9):​c.-123_-118+13delCGTGAGGTCAGTGCGGGGA variant causes a splice region change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: CASP9 NM_032996.3 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032996.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASP9	NM_032996.3		c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_region	Exon 1 of 9	NP_127463.2
	CASP9	NM_032996.3		c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_donor splice_region 5_prime_UTR intron	Exon 1 of 9	NP_127463.2
	CASP9	NM_032996.3		c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		non_coding_transcript	N/A	NP_127463.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASP9	ENST00000375890.8	TSL:2	c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_region	Exon 1 of 9	ENSP00000365051.4
	CASP9	ENST00000375890.8	TSL:2	c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_donor splice_region 5_prime_UTR intron	Exon 1 of 9	ENSP00000365051.4
	CASP9	ENST00000447522.5	TSL:3	c.-118+264_-118+282delCGTGAGGTCAGTGCGGGGA		intron	N/A	ENSP00000396540.1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4645982; hg19: chr1-15851064;