chr4-105235006-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001127208.3(TET2):c.1064G>A(p.Gly355Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0375 in 1,614,054 control chromosomes in the GnomAD database, including 1,339 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
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TET2 | NM_001127208.3 | c.1064G>A | p.Gly355Asp | missense_variant | 3/11 | ENST00000380013.9 | |
TET2-AS1 | NR_126420.1 | n.319-57334C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TET2 | ENST00000380013.9 | c.1064G>A | p.Gly355Asp | missense_variant | 3/11 | 5 | NM_001127208.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0281 AC: 4275AN: 152138Hom.: 89 Cov.: 32
GnomAD3 exomes AF: 0.0288 AC: 7213AN: 250800Hom.: 162 AF XY: 0.0292 AC XY: 3963AN XY: 135568
GnomAD4 exome AF: 0.0384 AC: 56182AN: 1461798Hom.: 1250 Cov.: 34 AF XY: 0.0381 AC XY: 27696AN XY: 727192
GnomAD4 genome AF: 0.0281 AC: 4272AN: 152256Hom.: 89 Cov.: 32 AF XY: 0.0263 AC XY: 1958AN XY: 74436
ClinVar
Submissions by phenotype
TET2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 13, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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