chr6-41198416-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024807.4(TREML2):c.69C>G(p.Asp23Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,595,472 control chromosomes in the GnomAD database, including 13,039 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.092 ( 794 hom., cov: 33)
Exomes 𝑓: 0.12 ( 12245 hom. )
Consequence
TREML2
NM_024807.4 missense
NM_024807.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.476
Genes affected
TREML2 (HGNC:21092): (triggering receptor expressed on myeloid cells like 2) TREML2 is located in a gene cluster on chromosome 6 with the single Ig variable (IgV) domain activating receptors TREM1 (MIM 605085) and TREM2 (MIM 605086), but it has distinct structural and functional properties (Allcock et al., 2003 [PubMed 12645956]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0015787482).
BP6
?
Variant 6-41198416-G-C is Benign according to our data. Variant chr6-41198416-G-C is described in ClinVar as [Benign]. Clinvar id is 769682.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREML2 | NM_024807.4 | c.69C>G | p.Asp23Glu | missense_variant | 2/5 | ENST00000483722.2 | |
TREML2 | XM_011514917.3 | c.55+2538C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREML2 | ENST00000483722.2 | c.69C>G | p.Asp23Glu | missense_variant | 2/5 | 1 | NM_024807.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0917 AC: 13947AN: 152100Hom.: 793 Cov.: 33
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GnomAD3 exomes AF: 0.0587 AC: 13148AN: 223886Hom.: 981 AF XY: 0.0593 AC XY: 7104AN XY: 119868
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GnomAD4 exome AF: 0.122 AC: 176617AN: 1443252Hom.: 12245 Cov.: 32 AF XY: 0.124 AC XY: 88684AN XY: 718028
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GnomAD4 genome ? AF: 0.0917 AC: 13959AN: 152220Hom.: 794 Cov.: 33 AF XY: 0.0902 AC XY: 6713AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of sheet (P = 0.0344);
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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