rs111948941
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001127208.3(TET2):c.100C>T(p.Leu34Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 1,614,044 control chromosomes in the GnomAD database, including 305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001127208.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TET2 | NM_001127208.3 | c.100C>T | p.Leu34Phe | missense_variant | 3/11 | ENST00000380013.9 | |
TET2-AS1 | NR_126420.1 | n.319-56370G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TET2 | ENST00000380013.9 | c.100C>T | p.Leu34Phe | missense_variant | 3/11 | 5 | NM_001127208.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0138 AC: 2097AN: 152158Hom.: 30 Cov.: 32
GnomAD3 exomes AF: 0.0156 AC: 3919AN: 250992Hom.: 46 AF XY: 0.0167 AC XY: 2268AN XY: 135638
GnomAD4 exome AF: 0.0171 AC: 24945AN: 1461768Hom.: 275 Cov.: 34 AF XY: 0.0174 AC XY: 12657AN XY: 727186
GnomAD4 genome ? AF: 0.0138 AC: 2100AN: 152276Hom.: 30 Cov.: 32 AF XY: 0.0138 AC XY: 1029AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at