2-74032462-T-TGTGTGTGTTTGTGTGTTGGTCGTGTGCGCGCGCCCCCCGCTCCCGCGCGCGATGGCCCAGCGGCTGGCAAGAGG

Position:

• chr2-74032462-T-TGTGTGTGTTTGTGTGTTGGTCGTGTGCGCGCGCCCCCCGCTCCCGCGCGCGATGGCCCAGCGGCTGGCAAGAGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001287491.2(TET3):​c.361-13808_361-13807insTTGTGTGTTGGTCGTGTGCGCGCGCCCCCCGCTCCCGCGCGCGATGGCCCAGCGGCTGGCAAGAGGGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 30)
• Consequence: TET3 NM_001287491.2 intron
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.387

Genes affected

TET3 (HGNC:28313): (tet methylcytosine dioxygenase 3) Enables methyl-CpG binding activity and zinc ion binding activity. Involved in histone H3-K4 trimethylation; positive regulation of transcription by RNA polymerase II; and protein O-linked glycosylation. Predicted to be located in cytoplasm and male pronucleus. Predicted to be active in nucleus. Biomarker of esophagus squamous cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TET3	NM_001287491.2	c.361-13808_361-13807insTTGTGTGTTGGTCGTGTGCGCGCGCCCCCCGCTCCCGCGCGCGATGGCCCAGCGGCTGGCAAGAGGGTGTGTGT		intron_variant		ENST00000409262.8	NP_001274420.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TET3	ENST00000409262.8	c.361-13808_361-13807insTTGTGTGTTGGTCGTGTGCGCGCGCCCCCCGCTCCCGCGCGCGATGGCCCAGCGGCTGGCAAGAGGGTGTGTGT		intron_variant		1	NM_001287491.2	ENSP00000386869.3
TET3	ENST00000305799.8	c.82-13808_82-13807insTTGTGTGTTGGTCGTGTGCGCGCGCCCCCCGCTCCCGCGCGCGATGGCCCAGCGGCTGGCAAGAGGGTGTGTGT		intron_variant		5		ENSP00000307803.8

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Schizophrenia Uncertain:1

Uncertain significance, no assertion criteria provided

case-control

Department of Psychiatry, The University of Hong Kong

Nov 11, 2022

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-74259589;