NM_001330078.2(NRXN1):c.772+1140G>A AND not specified

Germline classification:: Benign (4 submissions)
Last evaluated:: Jan 27, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000117842.14

Allele description [Variation Report for NM_001330078.2(NRXN1):c.772+1140G>A]

NM_001330078.2(NRXN1):c.772+1140G>A

Gene:

NRXN1:neurexin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_001330078.2(NRXN1):c.772+1140G>A

HGVS:

NC_000002.12:g.51026362C>T
NG_011878.1:g.11175G>A
NM_001135659.3:c.871+9G>A
NM_001330077.2:c.772+1140G>A
NM_001330078.2:c.772+1140G>AMANE SELECT
NM_001330079.2:c.772+1140G>A
NM_001330081.2:c.772+1140G>A
NM_001330082.2:c.772+1140G>A
NM_001330083.2:c.772+1140G>A
NM_001330084.2:c.772+1140G>A
NM_001330085.2:c.772+1140G>A
NM_001330086.2:c.772+1140G>A
NM_001330087.2:c.772+1140G>A
NM_001330088.2:c.772+1140G>A
NM_001330089.2:c.772+1140G>A
NM_001330090.2:c.772+1140G>A
NM_001330093.2:c.772+1140G>A
NM_001330094.2:c.772+1140G>A
NM_001330095.2:c.772+1140G>A
NM_001330096.2:c.772+1140G>A
NM_004801.6:c.772+1140G>A
NC_000002.11:g.51253500C>T
NM_001135659.1:c.871+9G>A
NM_001135659.2:c.871+9G>A

Links:

dbSNP: rs61658382

NCBI 1000 Genomes Browser:

rs61658382

Molecular consequence:

NM_001135659.3:c.871+9G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330077.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330078.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330079.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330081.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330082.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330083.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330084.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330085.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330086.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330087.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330088.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330089.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330090.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330093.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330094.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330095.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001330096.2:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_004801.6:c.772+1140G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000152113	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000170812	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jan 25, 2013)	germline	clinical testing	Citation Link,
SCV001475327	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Jan 27, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001984107	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jan 2, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000152113.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV000170812.11

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Athena Diagnostics, SCV001475327.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital, SCV001984107.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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