chr11-89710315-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001146162.1(TRIM77):c.17C>T(p.Thr6Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000327 in 1,527,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001146162.1 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 |
---|---|---|---|---|---|---|---|
TRIM77 | NM_001146162.1 | c.17C>T | p.Thr6Met | missense_variant | 1/6 | ENST00000398290.7 | |
TRIM77 | NM_001271942.1 | c.17C>T | p.Thr6Met | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM77 | ENST00000398290.7 | c.17C>T | p.Thr6Met | missense_variant | 1/6 | 5 | NM_001146162.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000644 AC: 10AN: 155342Hom.: 0 AF XY: 0.000110 AC XY: 9AN XY: 81710
GnomAD4 exome AF: 0.0000313 AC: 43AN: 1375636Hom.: 0 Cov.: 33 AF XY: 0.0000431 AC XY: 29AN XY: 672912
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.17C>T (p.T6M) alteration is located in exon 1 (coding exon 1) of the TRIM77 gene. This alteration results from a C to T substitution at nucleotide position 17, causing the threonine (T) at amino acid position 6 to be replaced by a methionine (M). 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