14-78243384-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001330195.2(NRXN3):c.291C>T(p.Ala97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000991 in 1,565,370 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0013 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00096 ( 6 hom. )
Consequence
NRXN3
NM_001330195.2 synonymous
NM_001330195.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.78
Genes affected
NRXN3 (HGNC:8010): (neurexin 3) This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants and protein isoforms for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. Genetic variation at this locus has been associated with a range of behavioral phenotypes, including alcohol dependence and autism spectrum disorder. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 14-78243384-C-T is Benign according to our data. Variant chr14-78243384-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3045674.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-4.78 with no splicing effect.
BS2
High AC in GnomAd4 at 194 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRXN3 | NM_001330195.2 | c.291C>T | p.Ala97= | synonymous_variant | 2/21 | ENST00000335750.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN3 | ENST00000335750.7 | c.291C>T | p.Ala97= | synonymous_variant | 2/21 | 5 | NM_001330195.2 | P1 | |
NRXN3 | ENST00000634499.2 | c.291C>T | p.Ala97= | synonymous_variant | 2/22 | 5 | |||
NRXN3 | ENST00000554738.5 | c.291C>T | p.Ala97= | synonymous_variant | 1/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00127 AC: 194AN: 152242Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00105 AC: 187AN: 178520Hom.: 0 AF XY: 0.000969 AC XY: 95AN XY: 98000
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GnomAD4 exome AF: 0.000961 AC: 1358AN: 1413010Hom.: 6 Cov.: 30 AF XY: 0.00105 AC XY: 732AN XY: 700106
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GnomAD4 genome AF: 0.00127 AC: 194AN: 152360Hom.: 1 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74510
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
NRXN3-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 24, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at