rs629508

chr11-95189235-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

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]

LNCRNA-IUR (HGNC:55755): (lncRNA imatinib upregulated)

ACMG classification

Verdict is Benign. Variant got -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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SESN3	NM_144665.4	c.525+544A>G		intron_variant		ENST00000536441.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SESN3	ENST00000536441.7	c.525+544A>G		intron_variant		2	NM_144665.4	P1
LNCRNA-IUR	ENST00000657854.2	n.508+31432T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44855 AN: 151624 Hom.: 7633 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.296 AC: 44861 AN: 151742 Hom.: 7636 Cov.: 32 AF XY: 0.299 AC XY: 22170 AN XY: 74156

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.313

Alfa AF: 0.353 Hom.: 13271

Bravo AF: 0.284

Asia WGS AF: 0.257 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs629508; hg19: chr11-94922399;