14-78703485-A-G
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.1222-5732A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,152 control chromosomes in the GnomAD database, including 25,231 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 0.53 ( 25231 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NRXN3
NM_001330195.2 intron
NM_001330195.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.651
Publications
6 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
Genome browser will be placed here
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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRXN3 | NM_001330195.2 | c.1222-5732A>G | intron_variant | Intron 6 of 20 | ENST00000335750.7 | NP_001317124.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRXN3 | ENST00000335750.7 | c.1222-5732A>G | intron_variant | Intron 6 of 20 | 5 | NM_001330195.2 | ENSP00000338349.7 |
Frequencies
GnomAD3 genomes AF: 0.532 AC: 80891AN: 152032Hom.: 25219 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
80891
AN:
152032
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
2
Hom.:
AF XY:
AC XY:
0
AN XY:
2
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
2
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome AF: 0.532 AC: 80916AN: 152152Hom.: 25231 Cov.: 33 AF XY: 0.537 AC XY: 39935AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
80916
AN:
152152
Hom.:
Cov.:
33
AF XY:
AC XY:
39935
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
7645
AN:
41520
American (AMR)
AF:
AC:
9552
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
2136
AN:
3472
East Asian (EAS)
AF:
AC:
2943
AN:
5174
South Asian (SAS)
AF:
AC:
2763
AN:
4820
European-Finnish (FIN)
AF:
AC:
7898
AN:
10586
Middle Eastern (MID)
AF:
AC:
164
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45979
AN:
67980
Other (OTH)
AF:
AC:
1166
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1601
3201
4802
6402
8003
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
686
1372
2058
2744
3430
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1929
AN:
3478
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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