chr9-26886793-T-C

Variant names:

• chr9-26886793-T-C
• rs17760820
• NM_024828.4:c.504+520A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024828.4(CAAP1):​c.504+520A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 152,256 control chromosomes in the GnomAD database, including 1,709 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 0.076 (1709 hom., cov: 33)
• Consequence: CAAP1 NM_024828.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 3 publications found

Genes affected

CAAP1 (HGNC:25834): (caspase activity and apoptosis inhibitor 1) Involved in negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024828.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAAP1	NM_024828.4	MANE Select	c.504+520A>G		intron	N/A	NP_079104.3
	CAAP1	NM_001167575.2		c.69+520A>G		intron	N/A	NP_001161047.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAAP1	ENST00000333916.8	TSL:1 MANE Select	c.504+520A>G		intron	N/A	ENSP00000369431.3
	CAAP1	ENST00000903808.1		c.504+520A>G		intron	N/A	ENSP00000573867.1
	CAAP1	ENST00000924906.1		c.504+520A>G		intron	N/A	ENSP00000594965.1

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11551 AN: 152138 Hom.: 1697 Cov.: 33

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0760 AC: 11575 AN: 152256 Hom.: 1709 Cov.: 33 AF XY: 0.0862 AC XY: 6417 AN XY: 74440

African (AFR) AF: 0.0335 AC: 1393 AN: 41570

American (AMR) AF: 0.151 AC: 2304 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3602 AN: 5172

South Asian (SAS) AF: 0.167 AC: 808 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1118 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0306 AC: 2081 AN: 68014

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0373 Hom.: 74

Bravo AF: 0.0838

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.5
DANN	Benign	0.81
PhyloP100		-0.073
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17760820; hg19: chr9-26886791;