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rs490192

Variant summary

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

The NM_015080.4(NRXN2):c.731-6105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,038 control chromosomes in the GnomAD database, including 10,544 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 0.33 ( 10544 hom., cov: 32)

Consequence

NRXN2
NM_015080.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.637
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NRXN2NM_015080.4 linkuse as main transcriptc.731-6105C>T intron_variant ENST00000265459.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NRXN2ENST00000265459.11 linkuse as main transcriptc.731-6105C>T intron_variant 5 NM_015080.4 P4Q9P2S2-1

Frequencies

GnomAD3 genomes
AF:
0.328
AC:
49812
AN:
151920
Hom.:
10512
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.595
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.240
Gnomad ASJ
AF:
0.167
Gnomad EAS
AF:
0.478
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.298
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.283
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.328
AC:
49886
AN:
152038
Hom.:
10544
Cov.:
32
AF XY:
0.329
AC XY:
24451
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.595
Gnomad4 AMR
AF:
0.241
Gnomad4 ASJ
AF:
0.167
Gnomad4 EAS
AF:
0.478
Gnomad4 SAS
AF:
0.210
Gnomad4 FIN
AF:
0.298
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.279
Alfa
AF:
0.273
Hom.:
1489
Bravo
AF:
0.336
Asia WGS
AF:
0.348
AC:
1210
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
Cadd
Benign
0.28
Dann
Benign
0.77

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: rs490192; hg19: chr11-64471369; API