chr11-5698547-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PVS1_StrongBP6_ModerateBS1BS2
The NM_006074.5(TRIM22):c.750+2T>C variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000902 in 1,610,064 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006074.5 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM22 | NM_006074.5 | c.750+2T>C | splice_donor_variant, intron_variant | Intron 4 of 7 | ENST00000379965.8 | NP_006065.2 | ||
TRIM22 | NM_001199573.2 | c.738+2T>C | splice_donor_variant, intron_variant | Intron 4 of 7 | NP_001186502.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00508 AC: 772AN: 152110Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00136 AC: 333AN: 244430Hom.: 2 AF XY: 0.000965 AC XY: 128AN XY: 132594
GnomAD4 exome AF: 0.000467 AC: 681AN: 1457836Hom.: 6 Cov.: 34 AF XY: 0.000381 AC XY: 276AN XY: 724748
GnomAD4 genome AF: 0.00506 AC: 771AN: 152228Hom.: 8 Cov.: 33 AF XY: 0.00446 AC XY: 332AN XY: 74440
ClinVar
Submissions by phenotype
TRIM22-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 08, 2021 | This variant is classified as likely 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 | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | TRIM22: BS1, BS2; TRIM5: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at