16-2060570-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000548.5(TSC2):​c.976-100C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 1,595,738 control chromosomes in the GnomAD database, including 257,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22385 hom., cov: 31)
Exomes 𝑓: 0.57 ( 234848 hom. )

Consequence

TSC2
NM_000548.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.93
Variant links:
Genes affected
TSC2 (HGNC:12363): (TSC complex subunit 2) This gene is a tumor suppressor gene that encodes the growth inhibitory protein tuberin. Tuberin interacts with hamartin to form the TSC protein complex which functions in the control of cell growth. This TSC protein complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 16-2060570-C-G is Benign according to our data. Variant chr16-2060570-C-G is described in ClinVar as [Benign]. Clinvar id is 675047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2060570-C-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSC2NM_000548.5 linkuse as main transcriptc.976-100C>G intron_variant ENST00000219476.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSC2ENST00000219476.9 linkuse as main transcriptc.976-100C>G intron_variant 5 NM_000548.5 P49815-1

Frequencies

GnomAD3 genomes
AF:
0.538
AC:
81643
AN:
151816
Hom.:
22360
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.442
Gnomad AMI
AF:
0.648
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.601
Gnomad EAS
AF:
0.713
Gnomad SAS
AF:
0.650
Gnomad FIN
AF:
0.542
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.577
Gnomad OTH
AF:
0.548
GnomAD4 exome
AF:
0.568
AC:
820770
AN:
1443804
Hom.:
234848
AF XY:
0.572
AC XY:
411257
AN XY:
718734
show subpopulations
Gnomad4 AFR exome
AF:
0.441
Gnomad4 AMR exome
AF:
0.468
Gnomad4 ASJ exome
AF:
0.600
Gnomad4 EAS exome
AF:
0.683
Gnomad4 SAS exome
AF:
0.649
Gnomad4 FIN exome
AF:
0.553
Gnomad4 NFE exome
AF:
0.565
Gnomad4 OTH exome
AF:
0.575
GnomAD4 genome
AF:
0.538
AC:
81701
AN:
151934
Hom.:
22385
Cov.:
31
AF XY:
0.539
AC XY:
39990
AN XY:
74224
show subpopulations
Gnomad4 AFR
AF:
0.442
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.601
Gnomad4 EAS
AF:
0.713
Gnomad4 SAS
AF:
0.651
Gnomad4 FIN
AF:
0.542
Gnomad4 NFE
AF:
0.577
Gnomad4 OTH
AF:
0.553
Alfa
AF:
0.444
Hom.:
1312
Bravo
AF:
0.526
Asia WGS
AF:
0.699
AC:
2429
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJul 15, 2024This variant is classified as Benign based on local population frequency. This variant was detected in 46% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 43. Only high quality variants are reported. -
Tuberous sclerosis 2 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 14, 2021- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.15
DANN
Benign
0.45

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: rs2074968; hg19: chr16-2110571; COSMIC: COSV54765122; COSMIC: COSV54765122; API