7-101088231-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030961.3(TRIM56):c.919G>A(p.Ala307Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,459,376 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_030961.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM56 | NM_030961.3 | c.919G>A | p.Ala307Thr | missense_variant | 3/3 | ENST00000306085.11 | |
TRIM56 | XM_011516589.4 | c.919G>A | p.Ala307Thr | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM56 | ENST00000306085.11 | c.919G>A | p.Ala307Thr | missense_variant | 3/3 | 1 | NM_030961.3 | P1 | |
TRIM56 | ENST00000412507.1 | c.816+103G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000144 AC: 1AN: 69490Hom.: 0 AF XY: 0.0000277 AC XY: 1AN XY: 36096
GnomAD4 exome AF: 0.0000168 AC: 22AN: 1307194Hom.: 0 Cov.: 73 AF XY: 0.0000204 AC XY: 13AN XY: 637146
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | The c.919G>A (p.A307T) alteration is located in exon 3 (coding exon 1) of the TRIM56 gene. This alteration results from a G to A substitution at nucleotide position 919, causing the alanine (A) at amino acid position 307 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