rs1973284

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005465.7(AKT3):​c.172+2212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 147,058 control chromosomes in the GnomAD database, including 23,623 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 0.53 ( 23623 hom., cov: 22)

Consequence

AKT3
NM_005465.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.400
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AKT3NM_005465.7 linkuse as main transcriptc.172+2212T>C intron_variant ENST00000673466.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AKT3ENST00000673466.1 linkuse as main transcriptc.172+2212T>C intron_variant NM_005465.7 P1Q9Y243-1

Frequencies

GnomAD3 genomes
AF:
0.526
AC:
77234
AN:
146950
Hom.:
23624
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.204
Gnomad AMI
AF:
0.729
Gnomad AMR
AF:
0.604
Gnomad ASJ
AF:
0.759
Gnomad EAS
AF:
0.403
Gnomad SAS
AF:
0.476
Gnomad FIN
AF:
0.611
Gnomad MID
AF:
0.627
Gnomad NFE
AF:
0.685
Gnomad OTH
AF:
0.575
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.525
AC:
77238
AN:
147058
Hom.:
23623
Cov.:
22
AF XY:
0.522
AC XY:
37271
AN XY:
71450
show subpopulations
Gnomad4 AFR
AF:
0.204
Gnomad4 AMR
AF:
0.604
Gnomad4 ASJ
AF:
0.759
Gnomad4 EAS
AF:
0.402
Gnomad4 SAS
AF:
0.476
Gnomad4 FIN
AF:
0.611
Gnomad4 NFE
AF:
0.685
Gnomad4 OTH
AF:
0.573
Alfa
AF:
0.571
Hom.:
3905
Bravo
AF:
0.511
Asia WGS
AF:
0.383
AC:
1327
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.3
DANN
Benign
0.81

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1973284; hg19: chr1-243856681; API