NM_000368.5:c.2626-3_2626-2insTTA

Variant names:

• chr9-132897612-T-TTAA
• rs760737807
• NM_000368.5:c.2626-3_2626-2insTTA

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The NM_000368.5(TSC1):​c.2626-3_2626-2insTTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000241 in 871,088 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: not found (cov: 14)
  • Exomes 𝑓: 0.000024 (0 hom.)
• Consequence: TSC1 NM_000368.5 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.387
• Publications: 0 publications found

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]

TSC1 Gene-Disease associations (from GenCC):

• tuberous sclerosis

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• tuberous sclerosis 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, PanelApp Australia, Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae)
• lung lymphangioleiomyomatosis

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• tuberous sclerosis complex

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP6: Variant 9-132897612-T-TTAA is Benign according to our data. Variant chr9-132897612-T-TTAA is described in ClinVar as Likely_benign. ClinVar VariationId is 3057832.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000368.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSC1	NM_000368.5	MANE Select	c.2626-3_2626-2insTTA		splice_region intron	N/A	NP_000359.1
	TSC1	NM_001406592.1		c.2626-3_2626-2insTTA		splice_region intron	N/A	NP_001393521.1
	TSC1	NM_001406593.1		c.2626-3_2626-2insTTA		splice_region intron	N/A	NP_001393522.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSC1	ENST00000298552.9	TSL:1 MANE Select	c.2626-3_2626-2insTTA		splice_region intron	N/A	ENSP00000298552.3
	TSC1	ENST00000490179.4	TSL:3	c.2626-3_2626-2insTTA		splice_region intron	N/A	ENSP00000495533.2
	TSC1	ENST00000643875.1		c.2626-3_2626-2insTTA		splice_region intron	N/A	ENSP00000495158.1

Frequencies

GnomAD3 genomes Cov.: 14

GnomAD4 exome AF: 0.0000241 AC: 21 AN: 871088 Hom.: 0 Cov.: 27 AF XY: 0.0000319 AC XY: 14 AN XY: 438620

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 23540

American (AMR) AF: 0.00 AC: 0 AN: 22736

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15378

East Asian (EAS) AF: 0.0000335 AC: 1 AN: 29840

South Asian (SAS) AF: 0.0000477 AC: 2 AN: 41888

European-Finnish (FIN) AF: 0.0000349 AC: 1 AN: 28654

Middle Eastern (MID) AF: 0.000311 AC: 1 AN: 3220

European-Non Finnish (NFE) AF: 0.0000165 AC: 11 AN: 668402

Other (OTH) AF: 0.000134 AC: 5 AN: 37430

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 14

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	TSC1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs760737807; hg19: chr9-135772999;