rs2865084

Positions:

• chr3-179146818-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125401.1(PIK3CA-DT):​n.58+1098T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,148 control chromosomes in the GnomAD database, including 893 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 0.089 (893 hom., cov: 32)
• Consequence: PIK3CA-DT NR_125401.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

Genes affected

PIK3CA-DT (HGNC:52932): (PIK3CA divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3CA-DT	NR_125401.1	n.58+1098T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3CA-DT	ENST00000435560.1	n.58+1098T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13544 AN: 152030 Hom.: 892 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0891 AC: 13552 AN: 152148 Hom.: 893 Cov.: 32 AF XY: 0.0849 AC XY: 6313 AN XY: 74392

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0725

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0168

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.0768 Hom.: 79

Bravo AF: 0.100

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2865084; hg19: chr3-178864606;