chr6-30108167-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007028.5(TRIM31):āc.769A>Gā(p.Ser257Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,598,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007028.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
TRIM31 | NM_007028.5 | c.769A>G | p.Ser257Gly | missense_variant, splice_region_variant | 6/9 | ENST00000376734.4 | |
TRIM31-AS1 | NR_126470.1 | n.273+380T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM31 | ENST00000376734.4 | c.769A>G | p.Ser257Gly | missense_variant, splice_region_variant | 6/9 | 5 | NM_007028.5 | P1 | |
TRIM31-AS1 | ENST00000440874.1 | n.273+380T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
TRIM31 | ENST00000468264.1 | n.33A>G | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
TRIM31 | ENST00000485864.5 | n.459A>G | splice_region_variant, non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000290 AC: 44AN: 151718Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246462Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134330
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1447030Hom.: 0 Cov.: 33 AF XY: 0.0000167 AC XY: 12AN XY: 720482
GnomAD4 genome AF: 0.000290 AC: 44AN: 151844Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.769A>G (p.S257G) alteration is located in exon 6 (coding exon 5) of the TRIM31 gene. This alteration results from a A to G substitution at nucleotide position 769, causing the serine (S) at amino acid position 257 to be replaced by a glycine (G). 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