chr1-228401056-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145214.3(TRIM11):c.643G>A(p.Ala215Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,612,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145214.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM11 | NM_145214.3 | c.643G>A | p.Ala215Thr | missense_variant | Exon 3 of 6 | ENST00000284551.11 | NP_660215.1 | |
TRIM11 | XM_017002412.3 | c.640G>A | p.Ala214Thr | missense_variant | Exon 3 of 6 | XP_016857901.1 | ||
TRIM11 | XM_011544285.4 | c.504+1010G>A | intron_variant | Intron 2 of 4 | XP_011542587.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000451 AC: 11AN: 243968Hom.: 0 AF XY: 0.0000376 AC XY: 5AN XY: 133032
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460150Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726410
GnomAD4 genome AF: 0.000158 AC: 24AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.643G>A (p.A215T) alteration is located in exon 3 (coding exon 3) of the TRIM11 gene. This alteration results from a G to A substitution at nucleotide position 643, causing the alanine (A) at amino acid position 215 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at