rs629508
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144665.4(SESN3):c.525+544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,742 control chromosomes in the GnomAD database, including 7,636 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 0.30 ( 7636 hom., cov: 32)
Consequence
SESN3
NM_144665.4 intron
NM_144665.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.533
Publications
3 publications found
Genes affected
SESN3 (HGNC:23060): (sestrin 3) This gene encodes a member of the sestrin family of stress-induced proteins. The encoded protein reduces the levels of intracellular reactive oxygen species induced by activated Ras downstream of RAC-alpha serine/threonine-protein kinase (Akt) and FoxO transcription factor. The protein is required for normal regulation of blood glucose, insulin resistance and plays a role in lipid storage in obesity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.296 AC: 44855AN: 151624Hom.: 7633 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
44855
AN:
151624
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.296 AC: 44861AN: 151742Hom.: 7636 Cov.: 32 AF XY: 0.299 AC XY: 22170AN XY: 74156 show subpopulations
GnomAD4 genome
AF:
AC:
44861
AN:
151742
Hom.:
Cov.:
32
AF XY:
AC XY:
22170
AN XY:
74156
show subpopulations
African (AFR)
AF:
AC:
5279
AN:
41464
American (AMR)
AF:
AC:
5178
AN:
15202
Ashkenazi Jewish (ASJ)
AF:
AC:
1107
AN:
3468
East Asian (EAS)
AF:
AC:
1432
AN:
5164
South Asian (SAS)
AF:
AC:
1432
AN:
4816
European-Finnish (FIN)
AF:
AC:
4569
AN:
10556
Middle Eastern (MID)
AF:
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
AC:
24495
AN:
67762
Other (OTH)
AF:
AC:
659
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1524
3048
4571
6095
7619
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
460
920
1380
1840
2300
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
898
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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