NM_002647.4:c.2649+5462C>T

Variant names:

• chr18-42072975-C-T
• rs1941526
• NM_002647.4:c.2649+5462C>T

Variant summary

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

The NM_002647.4(PIK3C3):​c.2649+5462C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,068 control chromosomes in the GnomAD database, including 5,064 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 0.25 (5064 hom., cov: 32)
• Consequence: PIK3C3 NM_002647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 4 publications found

Genes affected

PIK3C3 (HGNC:8974): (phosphatidylinositol 3-kinase catalytic subunit type 3) Enables 1-phosphatidylinositol-3-kinase activity. Involved in early endosome to late endosome transport and regulation of cytokinesis. Acts upstream of or within autophagy and protein lipidation. Located in autolysosome; late endosome; and midbody. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002647.4. 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
	PIK3C3	NM_002647.4	MANE Select	c.2649+5462C>T		intron	N/A	NP_002638.2
	PIK3C3	NM_001308020.2		c.2460+5462C>T		intron	N/A	NP_001294949.1	A8MYT4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3C3	ENST00000262039.9	TSL:1 MANE Select	c.2649+5462C>T		intron	N/A	ENSP00000262039.3	Q8NEB9
	PIK3C3	ENST00000858068.1		c.2643+5462C>T		intron	N/A	ENSP00000528127.1
	PIK3C3	ENST00000858070.1		c.2574+5462C>T		intron	N/A	ENSP00000528129.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38290 AN: 151950 Hom.: 5067 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.252 AC: 38302 AN: 152068 Hom.: 5064 Cov.: 32 AF XY: 0.255 AC XY: 18937 AN XY: 74354

African (AFR) AF: 0.203 AC: 8419 AN: 41490

American (AMR) AF: 0.339 AC: 5178 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1802 AN: 5160

South Asian (SAS) AF: 0.401 AC: 1938 AN: 4832

European-Finnish (FIN) AF: 0.208 AC: 2190 AN: 10552

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17059 AN: 67968

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.254 Hom.: 21155

Bravo AF: 0.259

Asia WGS AF: 0.365 AC: 1270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.50
PhyloP100		-0.56
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: rs1941526; hg19: chr18-39652939;