chr6-41282397-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018643.5(TREM1):āc.404A>Cā(p.Lys135Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,605,342 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 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 Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018643.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREM1 | NM_018643.5 | c.404A>C | p.Lys135Thr | missense_variant, splice_region_variant | 2/4 | ENST00000244709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREM1 | ENST00000244709.9 | c.404A>C | p.Lys135Thr | missense_variant, splice_region_variant | 2/4 | 1 | NM_018643.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00640 AC: 973AN: 152096Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00175 AC: 432AN: 246894Hom.: 6 AF XY: 0.00128 AC XY: 170AN XY: 133272
GnomAD4 exome AF: 0.000630 AC: 916AN: 1453128Hom.: 13 Cov.: 30 AF XY: 0.000535 AC XY: 386AN XY: 721796
GnomAD4 genome AF: 0.00644 AC: 980AN: 152214Hom.: 7 Cov.: 32 AF XY: 0.00634 AC XY: 472AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 13, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at