rs10150332

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001330195.2(NRXN3):​c.3444+3219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,022 control chromosomes in the GnomAD database, including 5,762 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 0.26 ( 5762 hom., cov: 32)

Consequence

NRXN3
NM_001330195.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NRXN3NM_001330195.2 linkuse as main transcriptc.3444+3219T>C intron_variant ENST00000335750.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NRXN3ENST00000335750.7 linkuse as main transcriptc.3444+3219T>C intron_variant 5 NM_001330195.2 P1

Frequencies

GnomAD3 genomes
AF:
0.256
AC:
38901
AN:
151904
Hom.:
5746
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.397
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.227
Gnomad ASJ
AF:
0.123
Gnomad EAS
AF:
0.000773
Gnomad SAS
AF:
0.116
Gnomad FIN
AF:
0.234
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.220
Gnomad OTH
AF:
0.227
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.256
AC:
38945
AN:
152022
Hom.:
5762
Cov.:
32
AF XY:
0.252
AC XY:
18708
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.397
Gnomad4 AMR
AF:
0.227
Gnomad4 ASJ
AF:
0.123
Gnomad4 EAS
AF:
0.000775
Gnomad4 SAS
AF:
0.115
Gnomad4 FIN
AF:
0.234
Gnomad4 NFE
AF:
0.220
Gnomad4 OTH
AF:
0.223
Alfa
AF:
0.220
Hom.:
1165
Bravo
AF:
0.263
Asia WGS
AF:
0.0830
AC:
291
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.24

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10150332; hg19: chr14-79936964; API