rs768765994
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001318810.2(SLITRK3):c.2582G>T(p.Arg861Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
SLITRK3
NM_001318810.2 missense
NM_001318810.2 missense
Scores
2
17
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.88
Genes affected
SLITRK3 (HGNC:23501): (SLIT and NTRK like family member 3) This gene encodes a member of the Slitrk family of structurally related transmembrane proteins that are involved in controlling neurite outgrowth. The encoded protein contains two leucine-rich repeat (LRR) domains and a C-terminal domain that is partially similar to Trk neurotrophin receptor protein. Enhanced expression of this gene was found in tissue from several different types of tumors. Alternative splicing results in multiple transcript variants, all encoding the same protein. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19385555).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLITRK3 | NM_001318810.2 | c.2582G>T | p.Arg861Leu | missense_variant | Exon 2 of 2 | ENST00000475390.2 | NP_001305739.1 | |
| SLITRK3 | NM_001318811.2 | c.2582G>T | p.Arg861Leu | missense_variant | Exon 2 of 2 | NP_001305740.1 | ||
| SLITRK3 | NM_014926.4 | c.2582G>T | p.Arg861Leu | missense_variant | Exon 2 of 2 | NP_055741.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLITRK3 | ENST00000475390.2 | c.2582G>T | p.Arg861Leu | missense_variant | Exon 2 of 2 | 1 | NM_001318810.2 | ENSP00000420091.1 | ||
| SLITRK3 | ENST00000241274.3 | c.2582G>T | p.Arg861Leu | missense_variant | Exon 2 of 2 | 1 | ENSP00000241274.3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461704Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727150
GnomAD4 exome
AF:
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1
AN:
1461704
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Cov.:
34
AF XY:
AC XY:
1
AN XY:
727150
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
31
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
D;D
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Gain of helix (P = 0.0143);Gain of helix (P = 0.0143);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at