2-50346870-GCGCCGCCGCCGCCGCCGCCGC-GCGCCGCCGCCGCCGCCGCCGCCGC

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP3BP6BS1

The NM_001330092.2(NRXN1):c.77_79dupGCG(p.Gly26dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000751 in 1,366,766 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A27A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00068 ( 1 hom. )

Consequence

NRXN1
NM_001330092.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:5

Conservation

PhyloP100: 1.48

Publications

0 publications found

Variant links:

Genes affected

NRXN1 (HGNC:8008): (neurexin 1) This gene encodes a single-pass type I membrane protein that belongs to the neurexin family. Neurexins are cell-surface receptors that bind neuroligins to form Ca(2+)-dependent neurexin/neuroligin complexes at synapses in the central nervous system. This complex is required for efficient neurotransmission and is involved in the formation of synaptic contacts. Three members of this gene family have been studied in detail and are estimated to generate over 3,000 variants through the use of two alternative promoters (alpha and beta) and extensive alternative splicing in each family member. Recently, a third promoter (gamma) was identified for this gene in the 3' region. Mutations in this gene are associated with Pitt-Hopkins-like syndrome-2 and may contribute to susceptibility to schizophrenia. [provided by RefSeq, Aug 2016]

NRXN1 Gene-Disease associations (from GenCC):

complex neurodevelopmental disorder
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
chromosome 2p16.3 deletion syndrome
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Pitt-Hopkins-like syndrome 2
Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
autism
Inheritance: AD Classification: MODERATE Submitted by: G2P
schizophrenia
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

NRXN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001330092.2

BP6

Variant 2-50346870-G-GCGC is Benign according to our data. Variant chr2-50346870-G-GCGC is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 282592.

BS1

Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0013 (196/150480) while in subpopulation EAS AF = 0.00276 (14/5078). AF 95% confidence interval is 0.00167. There are 0 homozygotes in GnomAd4. There are 103 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330092.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
NRXN1	NM_001330078.2	MANE Select	c.3365-109903_3365-109901dupGCG		intron	N/A	NP_001317007.1
NRXN1	NM_001330092.2		c.77_79dupGCG	p.Gly26dup	conservative_inframe_insertion	Exon 1 of 7	NP_001317021.1
NRXN1	NM_001330091.2		c.77_79dupGCG	p.Gly26dup	conservative_inframe_insertion	Exon 1 of 7	NP_001317020.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
NRXN1	ENST00000342183.9	TSL:1	c.77_79dupGCG	p.Gly26dup	conservative_inframe_insertion	Exon 1 of 6	ENSP00000341184.5
NRXN1	ENST00000401669.7	TSL:5 MANE Select	c.3365-109903_3365-109901dupGCG		intron	N/A	ENSP00000385017.2
NRXN1	ENST00000404971.5	TSL:1	c.3485-109903_3485-109901dupGCG		intron	N/A	ENSP00000385142.1

Frequencies

GnomAD3 genomes

AF:

0.00130

AC:

195

AN:

150380

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00177

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00119

Gnomad ASJ

AF:

0.00261

Gnomad EAS

AF:

0.00275

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.000299

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.000875

Gnomad OTH

AF:

0.00193

GnomAD4 exome

AF:

0.000683

AC:

831

AN:

1216286

Hom.:

Cov.:

AF XY:

0.000711

AC XY:

423

AN XY:

594980

show subpopulations

African (AFR)

AF:

0.00204

AC:

AN:

25490

American (AMR)

AF:

0.000706

AC:

AN:

15590

Ashkenazi Jewish (ASJ)

AF:

0.00113

AC:

AN:

19414

East Asian (EAS)

AF:

0.000785

AC:

AN:

28040

South Asian (SAS)

AF:

0.000784

AC:

AN:

44622

European-Finnish (FIN)

AF:

0.0000766

AC:

AN:

39152

Middle Eastern (MID)

AF:

0.00533

AC:

AN:

3940

European-Non Finnish (NFE)

AF:

0.000632

AC:

626

AN:

990732

Other (OTH)

AF:

0.000791

AC:

AN:

49306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.420

Heterozygous variant carriers

115

154

192

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00130

AC:

196

AN:

150480

Hom.:

Cov.:

AF XY:

0.00140

AC XY:

103

AN XY:

73468

show subpopulations

African (AFR)

AF:

0.00179

AC:

AN:

41302

American (AMR)

AF:

0.00119

AC:

AN:

15116

Ashkenazi Jewish (ASJ)

AF:

0.00261

AC:

AN:

3448

East Asian (EAS)

AF:

0.00276

AC:

AN:

5078

South Asian (SAS)

AF:

0.00166

AC:

AN:

4806

European-Finnish (FIN)

AF:

0.000299

AC:

AN:

10018

Middle Eastern (MID)

AF:

0.0240

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000875

AC:

AN:

67418

Other (OTH)

AF:

0.00191

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

ClinVar submissions as Germline

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Inborn genetic diseases (1)

NRXN1-related disorder (1)

Pitt-Hopkins-like syndrome 2 (1)

Pitt-Hopkins-like syndrome 2;C3808494:Chromosome 2p16.3 deletion syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.5

Mutation Taster

=78/22

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over