rs1324262269
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_015080.4(NRXN2):āc.359A>Cā(p.Asp120Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000261 in 1,380,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000086 ( 0 hom., cov: 33)
Exomes š: 0.000019 ( 0 hom. )
Consequence
NRXN2
NM_015080.4 missense
NM_015080.4 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 3.91
Genes affected
NRXN2 (HGNC:8009): (neurexin 2) This gene encodes a member of the neurexin gene family. The products of these genes function as cell adhesion molecules and receptors in the vertebrate nervous system. These genes utilize two promoters. The majority of transcripts are produced from the upstream promoter and encode alpha-neurexin isoforms while a smaller number of transcripts are produced from the downstream promoter and encode beta-neuresin isoforms. The alpha-neurexins contain epidermal growth factor-like (EGF-like) sequences and laminin G domains, and have been shown to interact with neurexophilins. The beta-neurexins lack EGF-like sequences and contain fewer laminin G domains than alpha-neurexins. Alternative splicing and the use of alternative promoters may generate thousands of transcript variants (PMID: 12036300, PMID: 11944992).[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.41313246).
BP6
Variant 11-64713341-T-G is Benign according to our data. Variant chr11-64713341-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 436059.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRXN2 | NM_015080.4 | c.359A>C | p.Asp120Ala | missense_variant | 2/23 | ENST00000265459.11 | NP_055895.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRXN2 | ENST00000265459.11 | c.359A>C | p.Asp120Ala | missense_variant | 2/23 | 5 | NM_015080.4 | ENSP00000265459 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000859 AC: 13AN: 151326Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000187 AC: 23AN: 1229636Hom.: 0 Cov.: 34 AF XY: 0.0000283 AC XY: 17AN XY: 601670
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GnomAD4 genome AF: 0.0000859 AC: 13AN: 151326Hom.: 0 Cov.: 33 AF XY: 0.0000947 AC XY: 7AN XY: 73944
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 15, 2016 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T;T
Sift4G
Uncertain
D;D;D;D
Polyphen
P;P;P;.
Vest4
MutPred
Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);
MVP
MPC
0.77
ClinPred
T
GERP RS
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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