chr11-5708197-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006074.5(TRIM22):āc.798G>Cā(p.Lys266Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_006074.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM22 | NM_006074.5 | c.798G>C | p.Lys266Asn | missense_variant | 6/8 | ENST00000379965.8 | |
TRIM22 | NM_001199573.2 | c.786G>C | p.Lys262Asn | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM22 | ENST00000379965.8 | c.798G>C | p.Lys266Asn | missense_variant | 6/8 | 1 | NM_006074.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000802 AC: 20AN: 249526Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135372
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727222
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.798G>C (p.K266N) alteration is located in exon 6 (coding exon 5) of the TRIM22 gene. This alteration results from a G to C substitution at nucleotide position 798, causing the lysine (K) at amino acid position 266 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
TRIM22-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 11, 2022 | The TRIM22 c.798G>C variant is predicted to result in the amino acid substitution p.Lys266Asn. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.092% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-5729427-G-C). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at