14-78243384-C-T

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

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -4.78
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]

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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
NRXN3NM_001330195.2 linkuse as main transcriptc.291C>T p.Ala97= synonymous_variant 2/21 ENST00000335750.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NRXN3ENST00000335750.7 linkuse as main transcriptc.291C>T p.Ala97= synonymous_variant 2/215 NM_001330195.2 P1
NRXN3ENST00000634499.2 linkuse as main transcriptc.291C>T p.Ala97= synonymous_variant 2/225
NRXN3ENST00000554738.5 linkuse as main transcriptc.291C>T p.Ala97= synonymous_variant 1/205 Q9Y4C0-4

Frequencies

GnomAD3 genomes
AF:
0.00127
AC:
194
AN:
152242
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00207
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00234
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.00105
AC:
187
AN:
178520
Hom.:
0
AF XY:
0.000969
AC XY:
95
AN XY:
98000
show subpopulations
Gnomad AFR exome
AF:
0.000207
Gnomad AMR exome
AF:
0.000140
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00262
Gnomad NFE exome
AF:
0.00188
Gnomad OTH exome
AF:
0.00199
GnomAD4 exome
AF:
0.000961
AC:
1358
AN:
1413010
Hom.:
6
Cov.:
30
AF XY:
0.00105
AC XY:
732
AN XY:
700106
show subpopulations
Gnomad4 AFR exome
AF:
0.000367
Gnomad4 AMR exome
AF:
0.000176
Gnomad4 ASJ exome
AF:
0.000118
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000123
Gnomad4 FIN exome
AF:
0.00322
Gnomad4 NFE exome
AF:
0.00104
Gnomad4 OTH exome
AF:
0.00130
GnomAD4 genome
AF:
0.00127
AC:
194
AN:
152360
Hom.:
1
Cov.:
32
AF XY:
0.00132
AC XY:
98
AN XY:
74510
show subpopulations
Gnomad4 AFR
AF:
0.000240
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00207
Gnomad4 NFE
AF:
0.00234
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00445
Hom.:
1
Bravo
AF:
0.000827

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 providedclinical testingPreventionGenetics, part of Exact SciencesOct 24, 2022This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.39
DANN
Benign
0.63

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: rs138817150; hg19: chr14-78709727; API