chr7-28956431-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014817.4(TRIL):c.1616C>A(p.Ala539Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,540,590 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014817.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIL | NM_014817.4 | c.1616C>A | p.Ala539Glu | missense_variant | 1/1 | ENST00000539664.3 | NP_055632.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIL | ENST00000539664.3 | c.1616C>A | p.Ala539Glu | missense_variant | 1/1 | NM_014817.4 | ENSP00000479256 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152232Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000176 AC: 24AN: 136708Hom.: 0 AF XY: 0.000173 AC XY: 13AN XY: 75254
GnomAD4 exome AF: 0.000218 AC: 303AN: 1388358Hom.: 1 Cov.: 32 AF XY: 0.000226 AC XY: 155AN XY: 685844
GnomAD4 genome AF: 0.000217 AC: 33AN: 152232Hom.: 0 Cov.: 34 AF XY: 0.000202 AC XY: 15AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.1616C>A (p.A539E) alteration is located in exon 1 (coding exon 1) of the TRIL gene. This alteration results from a C to A substitution at nucleotide position 1616, causing the alanine (A) at amino acid position 539 to be replaced by a glutamic acid (E). 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