4-105236713-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001127208.3(TET2):c.2771A>G(p.His924Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00131 in 1,614,148 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_001127208.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TET2 | NM_001127208.3 | c.2771A>G | p.His924Arg | missense_variant | Exon 3 of 11 | ENST00000380013.9 | NP_001120680.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00679 AC: 1034AN: 152216Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.00182 AC: 456AN: 250726Hom.: 7 AF XY: 0.00123 AC XY: 166AN XY: 135460
GnomAD4 exome AF: 0.000733 AC: 1072AN: 1461814Hom.: 18 Cov.: 34 AF XY: 0.000645 AC XY: 469AN XY: 727208
GnomAD4 genome AF: 0.00680 AC: 1036AN: 152334Hom.: 16 Cov.: 32 AF XY: 0.00612 AC XY: 456AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
not specified Benign:1Other:1
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at