chr6-30112425-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007028.5(TRIM31):c.381T>A(p.Asn127Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N127D) has been classified as Benign.
Frequency
Consequence
NM_007028.5 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 |
---|---|---|---|---|---|---|---|
TRIM31 | NM_007028.5 | c.381T>A | p.Asn127Lys | missense_variant | 2/9 | ENST00000376734.4 | |
TRIM31-AS1 | NR_126470.1 | n.395+586A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM31 | ENST00000376734.4 | c.381T>A | p.Asn127Lys | missense_variant | 2/9 | 5 | NM_007028.5 | P1 | |
TRIM31-AS1 | ENST00000440874.1 | n.395+586A>T | intron_variant, non_coding_transcript_variant | 3 | |||||
TRIM31 | ENST00000493404.1 | n.51T>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460598Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726612
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.381T>A (p.N127K) alteration is located in exon 2 (coding exon 1) of the TRIM31 gene. This alteration results from a T to A substitution at nucleotide position 381, causing the asparagine (N) at amino acid position 127 to be replaced by a lysine (K). 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