Genetic Variant NRXN1:p.Gly24_Gly26del (chr2-50346870-GCGCCGCCGC-G) – ACMG Classification: Benign (-17 pts)

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2

The NM_001330092.2(NRXN1):c.71_79delGCGGCGGCG(p.Gly24_Gly26del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000902 in 1,366,786 control chromosomes in the GnomAD database, including 37 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0028 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00066 ( 37 hom. )

Consequence

NRXN1
NM_001330092.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 3.96

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001330092.2

BP6

Variant 2-50346870-GCGCCGCCGC-G is Benign according to our data. Variant chr2-50346870-GCGCCGCCGC-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 281242.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00282 (425/150480) while in subpopulation AFR AF = 0.00855 (353/41300). AF 95% confidence interval is 0.00781. There are 0 homozygotes in GnomAd4. There are 206 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAdExome4 at 37 AR,AD,Unknown gene

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.3365-109909_3365-109901delGCGGCGGCG		intron	N/A	NP_001317007.1
NRXN1	NM_001330092.2		c.71_79delGCGGCGGCG	p.Gly24_Gly26del	disruptive_inframe_deletion	Exon 1 of 7	NP_001317021.1
NRXN1	NM_001330091.2		c.71_79delGCGGCGGCG	p.Gly24_Gly26del	disruptive_inframe_deletion	Exon 1 of 7	NP_001317020.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
NRXN1	ENST00000342183.9	TSL:1	c.71_79delGCGGCGGCG	p.Gly24_Gly26del	disruptive_inframe_deletion	Exon 1 of 6	ENSP00000341184.5
NRXN1	ENST00000401669.7	TSL:5 MANE Select	c.3365-109909_3365-109901delGCGGCGGCG		intron	N/A	ENSP00000385017.2
NRXN1	ENST00000404971.5	TSL:1	c.3485-109909_3485-109901delGCGGCGGCG		intron	N/A	ENSP00000385142.1

Frequencies

GnomAD3 genomes

AF:

0.00280

AC:

421

AN:

150380

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00847

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00232

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000393

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000341

Gnomad OTH

AF:

0.00145

GnomAD2 exomes

AF:

0.00148

AC:

111

AN:

74950

AF XY:

0.00160

show subpopulations

Gnomad AFR exome

AF:

0.00305

Gnomad AMR exome

AF:

0.00646

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00466

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000290

Gnomad OTH exome

AF:

0.00108

GnomAD4 exome

AF:

0.000664

AC:

808

AN:

1216306

Hom.:

AF XY:

0.000748

AC XY:

445

AN XY:

594994

show subpopulations

African (AFR)

AF:

0.00808

AC:

206

AN:

25486

American (AMR)

AF:

0.00436

AC:

AN:

15590

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19418

East Asian (EAS)

AF:

0.00136

AC:

AN:

28040

South Asian (SAS)

AF:

0.00531

AC:

237

AN:

44626

European-Finnish (FIN)

AF:

0.0000255

AC:

AN:

39152

Middle Eastern (MID)

AF:

0.000507

AC:

AN:

3942

European-Non Finnish (NFE)

AF:

0.000208

AC:

206

AN:

990746

Other (OTH)

AF:

0.00101

AC:

AN:

49306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.621

Heterozygous variant carriers

113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.00282

AC:

425

AN:

150480

Hom.:

Cov.:

AF XY:

0.00280

AC XY:

206

AN XY:

73466

show subpopulations

African (AFR)

AF:

0.00855

AC:

353

AN:

41300

American (AMR)

AF:

0.00232

AC:

AN:

15118

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3448

East Asian (EAS)

AF:

0.000394

AC:

AN:

5078

South Asian (SAS)

AF:

0.00187

AC:

AN:

4806

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10018

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000341

AC:

AN:

67418

Other (OTH)

AF:

0.00144

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

120

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:

0.000111

Hom.:

Bravo

AF:

0.00306

ClinVar

ClinVar submissions as Germline

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Inborn genetic diseases (1)

not specified (1)

NRXN1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.0

Mutation Taster

=197/3

polymorphism

(source)

Splicing

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

Publications

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2-50346870-GCGCCGCCGCCGCCGCCGCCGC-GCGCCGCCGCCGC

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