rs3827665

chr9-132929522-G-A

Variant summary

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

The NM_000368.5(TSC1):c.-80-570C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 152,182 control chromosomes in the GnomAD database, including 638 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 0.092 (638 hom., cov: 32)
• Consequence: TSC1 NM_000368.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

TSC1 (HGNC:12362): (TSC complex subunit 1) This gene is a tumor suppressor gene that encodes the growth inhibitory protein hamartin. The encoded protein interacts with and stabilizes the GTPase activating protein tuberin. This hamartin-tuberin complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. This protein also functions as a co-chaperone for Hsp90 that inhibits its ATPase activity. This protein functions as a facilitator of Hsp90-mediated folding of kinase and non-kinase clients, including TSC2 and thereby preventing their ubiquitination and proteasomal degradation. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSC1	NM_000368.5	c.-80-570C>T		intron_variant		ENST00000298552.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSC1	ENST00000298552.9	c.-80-570C>T		intron_variant		1	NM_000368.5	P4

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14019 AN: 152062 Hom.: 637 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0922 AC: 14030 AN: 152182 Hom.: 638 Cov.: 32 AF XY: 0.0894 AC XY: 6652 AN XY: 74432

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.0773

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.0779

Gnomad4 FIN AF: 0.0861

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.0888

Alfa AF: 0.0992 Hom.: 118

Bravo AF: 0.0906

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.4
Dann	Benign	0.37

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

Other links and lift over

dbSNP: rs3827665; hg19: chr9-135804909;