6-30340273-A-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The ENST00000396547.5(TRIM39):c.805A>C(p.Asn269His) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000546 in 1,612,654 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/22 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 Likely benign (★).
Frequency
Consequence
ENST00000396547.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM39 | NM_001369521.2 | c.804-232A>C | intron_variant | ENST00000396551.9 | |||
TRIM39-RPP21 | NM_001199119.1 | c.804-232A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM39 | ENST00000396551.9 | c.804-232A>C | intron_variant | 5 | NM_001369521.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000770 AC: 19AN: 246710Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134440
GnomAD4 exome AF: 0.0000548 AC: 80AN: 1460396Hom.: 1 Cov.: 31 AF XY: 0.0000592 AC XY: 43AN XY: 726554
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at