rs4645982

Variant names:

• chr1-15524569-ATCCCCGCACTGACCTCACG-A
• 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. Variant got 0 ACMG points: 0P and 0B.

The NM_032996.3(CASP9):​c.-123_-118+13delCGTGAGGTCAGTGCGGGGA variant causes a splice donor, splice region, 5 prime UTR, intron change involving the alteration of a non-conserved nucleotide. 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_donor, splice_region, 5_prime_UTR, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASP9	NM_032996.3	c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_region_variant	Exon 1 of 9		NP_127463.2
CASP9	NM_032996.3	c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_donor_variant, splice_region_variant, 5_prime_UTR_variant, intron_variant	Exon 1 of 9		NP_127463.2
CASP9	XM_005246014.3	c.-118+264_-118+282delCGTGAGGTCAGTGCGGGGA		intron_variant	Intron 1 of 8		XP_005246071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASP9	ENST00000375890.8	c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_region_variant	Exon 1 of 9	2		ENSP00000365051.4
CASP9	ENST00000375890.8	c.-123_-118+13delCGTGAGGTCAGTGCGGGGA		splice_donor_variant, splice_region_variant, 5_prime_UTR_variant, intron_variant	Exon 1 of 9	2		ENSP00000365051.4
CASP9	ENST00000447522.5	c.-118+264_-118+282delCGTGAGGTCAGTGCGGGGA		intron_variant	Intron 1 of 6	3		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 v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-15851064;