rs4132509

Variant names:

• chr1-243779782-C-A
• rs4132509
• NM_005465.7:c.46+63343G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-243779782-C-A
• chr1-243779782-C-G
• chr1-243779782-C-T

Variant summary

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

The NM_005465.7(AKT3):​c.46+63343G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,814 control chromosomes in the GnomAD database, including 4,381 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 0.23 (4381 hom., cov: 32)
• Consequence: AKT3 NM_005465.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

Genes affected

AKT3 (HGNC:393): (AKT serine/threonine kinase 3) The protein encoded by this gene is a member of the AKT, also called PKB, serine/threonine protein kinase family. AKT kinases are known to be regulators of cell signaling in response to insulin and growth factors. They are involved in a wide variety of biological processes including cell proliferation, differentiation, apoptosis, tumorigenesis, as well as glycogen synthesis and glucose uptake. This kinase has been shown to be stimulated by platelet-derived growth factor (PDGF), insulin, and insulin-like growth factor 1 (IGF1). Alternatively splice transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKT3	NM_005465.7	c.46+63343G>T		intron_variant	Intron 2 of 13	ENST00000673466.1	NP_005456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKT3	ENST00000673466.1	c.46+63343G>T		intron_variant	Intron 2 of 13		NM_005465.7	ENSP00000500582.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34889 AN: 151696 Hom.: 4371 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.230 AC: 34947 AN: 151814 Hom.: 4381 Cov.: 32 AF XY: 0.235 AC XY: 17420 AN XY: 74188

African (AFR) AF: 0.304 AC: 12596 AN: 41416

American (AMR) AF: 0.220 AC: 3358 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1186 AN: 4810

European-Finnish (FIN) AF: 0.230 AC: 2425 AN: 10532

Middle Eastern (MID) AF: 0.194 AC: 56 AN: 288

European-Non Finnish (NFE) AF: 0.185 AC: 12575 AN: 67850

Other (OTH) AF: 0.227 AC: 478 AN: 2106

Alfa AF: 0.196 Hom.: 11377

Bravo AF: 0.233

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.74
PhyloP100		-0.41
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

Publications

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Other links and lift over

dbSNP: rs4132509; hg19: chr1-243943084;