rs368959516
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001142699.3(DLG2):āc.2618G>Cā(p.Arg873Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000689 in 1,450,996 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes š: 6.9e-7 ( 0 hom. )
Consequence
DLG2
NM_001142699.3 missense, splice_region
NM_001142699.3 missense, splice_region
Scores
3
8
8
Splicing: ADA: 0.9896
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.79
Genes affected
DLG2 (HGNC:2901): (discs large MAGUK scaffold protein 2) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. The encoded protein forms a heterodimer with a related family member that may interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins. Multiple transcript variants encoding different isoforms have been found for this gene. Additional transcript variants have been described, but their full-length nature is not known. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242352Hom.: 0 AF XY: 0.00000759 AC XY: 1AN XY: 131690
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GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450996Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 721474
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721474
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
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AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T;.;.;.;.;.;T;T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;.;.;.;.;.;.;.;.;.;.
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;.;.;D;D;D;D;D;D;D
REVEL
Benign
Sift
Benign
T;T;T;.;.;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;.;.;T;T;T;T;T;T;.
Polyphen
0.27, 0.96, 1.0, 0.060, 0.086, 0.98
.;B;.;.;.;D;D;B;B;D;D;.
Vest4
MutPred
0.40
.;Loss of MoRF binding (P = 0.0509);.;.;.;.;.;.;.;.;.;.;
MVP
MPC
2.0
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at