chr4-184646777-C-T

Variant names:

• chr4-184646777-C-T
• rs4647610
• NM_004346.4:c.-16+1688G>A

Variant summary

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

The NM_004346.4(CASP3):​c.-16+1688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 150,450 control chromosomes in the GnomAD database, including 3,173 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 0.17 (3173 hom., cov: 30)
• Consequence: CASP3 NM_004346.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 20 publications found

Genes affected

CASP3 (HGNC:1504): (caspase 3) The protein encoded by this gene is a cysteine-aspartic acid protease that plays a central role in the execution-phase of cell apoptosis. The encoded protein cleaves and inactivates poly(ADP-ribose) polymerase while it cleaves and activates sterol regulatory element binding proteins as well as caspases 6, 7, and 9. This protein itself is processed by caspases 8, 9, and 10. It is the predominant caspase involved in the cleavage of amyloid-beta 4A precursor protein, which is associated with neuronal death in Alzheimer's disease. [provided by RefSeq, Aug 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASP3	NM_004346.4	c.-16+1688G>A		intron_variant	Intron 2 of 7	ENST00000308394.9	NP_004337.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASP3	ENST00000308394.9	c.-16+1688G>A		intron_variant	Intron 2 of 7	1	NM_004346.4	ENSP00000311032.4

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25563 AN: 150334 Hom.: 3169 Cov.: 30

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.170 AC: 25580 AN: 150450 Hom.: 3173 Cov.: 30 AF XY: 0.178 AC XY: 13046 AN XY: 73438

African (AFR) AF: 0.112 AC: 4536 AN: 40400

American (AMR) AF: 0.297 AC: 4488 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3466 AN: 5138

South Asian (SAS) AF: 0.301 AC: 1426 AN: 4730

European-Finnish (FIN) AF: 0.140 AC: 1464 AN: 10446

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9188 AN: 67882

Other (OTH) AF: 0.161 AC: 336 AN: 2088

Alfa AF: 0.148 Hom.: 2523

Bravo AF: 0.181

Asia WGS AF: 0.445 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.11
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: rs4647610; hg19: chr4-185567931;