NM_133433.4(NIPBL):c.256G>A (p.Asp86Asn) AND Inborn genetic diseases

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 16, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002777412.2

Allele description [Variation Report for NM_133433.4(NIPBL):c.256G>A (p.Asp86Asn)]

NM_133433.4(NIPBL):c.256G>A (p.Asp86Asn)

Gene:

NIPBL:NIPBL cohesin loading factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_133433.4(NIPBL):c.256G>A (p.Asp86Asn)

HGVS:

NC_000005.10:g.36958129G>A
NG_006987.2:g.86247G>A
NM_015384.5:c.256G>A
NM_133433.4:c.256G>AMANE SELECT
NP_056199.2:p.Asp86Asn
NP_597677.2:p.Asp86Asn
NC_000005.9:g.36958231G>A
NM_133433.3:c.256G>A

Protein change:

D86N

Molecular consequence:

NM_015384.5:c.256G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_133433.4:c.256G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003580017	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Dec 16, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 28518168, 32461654 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003580017

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Dec 16, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Using high-resolution variant frequencies to empower clinical genome interpretation.

Whiffin N, Minikel E, Walsh R, O'Donnell-Luria AH, Karczewski K, Ing AY, Barton PJR, Funke B, Cook SA, MacArthur D, Ware JS.

Genet Med. 2017 Oct;19(10):1151-1158. doi: 10.1038/gim.2017.26. Epub 2017 May 18.

PubMed [citation]

PMID:: 28518168
PMCID:: PMC5563454

The mutational constraint spectrum quantified from variation in 141,456 humans.

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, Gauthier LD, Brand H, Solomonson M, Watts NA, Rhodes D, Singer-Berk M, England EM, Seaby EG, Kosmicki JA, Walters RK, Tashman K, Farjoun Y, et al.

Nature. 2020 May;581(7809):434-443. doi: 10.1038/s41586-020-2308-7. Epub 2020 May 27. Erratum in: Nature. 2021 Feb;590(7846):E53. doi: 10.1038/s41586-020-03174-8. Nature. 2021 Sep;597(7874):E3-E4. doi: 10.1038/s41586-021-03758-y.

PubMed [citation]

PMID:: 32461654
PMCID:: PMC7334197

Details of each submission

From Ambry Genetics, SCV003580017.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

Last Updated: May 1, 2024

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