chr6-41278735-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018643.5(TREM1):c.599+2226A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,982 control chromosomes in the GnomAD database, including 41,393 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.73 ( 41393 hom., cov: 31)
Consequence
TREM1
NM_018643.5 intron
NM_018643.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.393
Genes affected
TREM1 (HGNC:17760): (triggering receptor expressed on myeloid cells 1) This gene encodes a receptor belonging to the Ig superfamily that is expressed on myeloid cells. This protein amplifies neutrophil and monocyte-mediated inflammatory responses triggered by bacterial and fungal infections by stimulating release of pro-inflammatory chemokines and cytokines, as well as increased surface expression of cell activation markers. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREM1 | NM_018643.5 | c.599+2226A>G | intron_variant | ENST00000244709.9 | |||
TREM1 | NM_001242590.3 | c.407-2505A>G | intron_variant | ||||
TREM1 | XM_011514696.3 | c.599+2226A>G | intron_variant | ||||
TREM1 | NR_136332.2 | n.626+2226A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREM1 | ENST00000244709.9 | c.599+2226A>G | intron_variant | 1 | NM_018643.5 | P2 | |||
TREM1 | ENST00000334475.10 | c.407-2505A>G | intron_variant | 1 | A2 | ||||
TREM1 | ENST00000589614.5 | c.599+2226A>G | intron_variant | 2 | A2 | ||||
TREM1 | ENST00000589695.1 | n.274+2226A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.730 AC: 110934AN: 151866Hom.: 41342 Cov.: 31
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GnomAD4 genome ? AF: 0.731 AC: 111041AN: 151982Hom.: 41393 Cov.: 31 AF XY: 0.723 AC XY: 53685AN XY: 74246
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1869
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at