chr14-78365884-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001330195.2(NRXN3):c.757+68024G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 152,196 control chromosomes in the GnomAD database, including 777 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.090 ( 777 hom., cov: 33)
Consequence
NRXN3
NM_001330195.2 intron
NM_001330195.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.348
Publications
1 publications found
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]
NRXN3 Gene-Disease associations (from GenCC):
- autismInheritance: AD Classification: LIMITED Submitted by: G2P
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRXN3 | NM_001330195.2 | c.757+68024G>A | intron_variant | Intron 4 of 20 | ENST00000335750.7 | NP_001317124.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRXN3 | ENST00000335750.7 | c.757+68024G>A | intron_variant | Intron 4 of 20 | 5 | NM_001330195.2 | ENSP00000338349.7 |
Frequencies
GnomAD3 genomes AF: 0.0903 AC: 13729AN: 152078Hom.: 775 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
13729
AN:
152078
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0903 AC: 13748AN: 152196Hom.: 777 Cov.: 33 AF XY: 0.0912 AC XY: 6785AN XY: 74408 show subpopulations
GnomAD4 genome
AF:
AC:
13748
AN:
152196
Hom.:
Cov.:
33
AF XY:
AC XY:
6785
AN XY:
74408
show subpopulations
African (AFR)
AF:
AC:
4362
AN:
41522
American (AMR)
AF:
AC:
1509
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
146
AN:
3468
East Asian (EAS)
AF:
AC:
1450
AN:
5164
South Asian (SAS)
AF:
AC:
318
AN:
4822
European-Finnish (FIN)
AF:
AC:
904
AN:
10608
Middle Eastern (MID)
AF:
AC:
15
AN:
292
European-Non Finnish (NFE)
AF:
AC:
4844
AN:
68014
Other (OTH)
AF:
AC:
150
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
651
1301
1952
2602
3253
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
150
300
450
600
750
<30
30-35
35-40
40-45
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50-55
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
534
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
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
Publications
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