Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001005373.4(LRSAM1):c.268G>A (p.Asp90Asn)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 25, 2021)
Last evaluated:
Nov 17, 2020
Accession:
VCV000234345.17
Variation ID:
234345
Description:
single nucleotide variant
Help

NM_001005373.4(LRSAM1):c.268G>A (p.Asp90Asn)

Allele ID
231715
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q33.3
Genomic location
9: 127459018 (GRCh38) GRCh38 UCSC
9: 130221297 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_373:g.12533G>A
LRG_373t1:c.268G>A LRG_373p1:p.Asp90Asn
NC_000009.12:g.127459018G>A
... more HGVS
Protein change
D90N
Other names
-
Canonical SPDI
NC_000009.12:127459017:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD) 0.00133
Exome Aggregation Consortium (ExAC) 0.00134
The Genome Aggregation Database (gnomAD), exomes 0.00128
The Genome Aggregation Database (gnomAD) 0.00137
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00177
Trans-Omics for Precision Medicine (TOPMed) 0.00117
Trans-Omics for Precision Medicine (TOPMed) 0.00140
Links
ClinGen: CA5246483
dbSNP: rs117692127
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 17, 2020 RCV001001954.6
Likely benign 1 criteria provided, single submitter - RCV001174265.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Apr 5, 2019 RCV000416142.6
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LRSAM1 - - GRCh38
GRCh37
522 561

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 17, 2020)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease type 2P
Allele origin: germline
Invitae
Accession: SCV000558965.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Apr 05, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000279018.7
Submitted: (Sep 25, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 32376792)
Uncertain significance
(Aug 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000493555.13
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease
Allele origin: germline
Molecular Genetics Laboratory,London Health Sciences Centre
Accession: SCV001337395.1
Submitted: (Apr 07, 2020)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease type 2P
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001331068.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Sep 05, 2019)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease type 2P
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001159747.2
Submitted: (Dec 11, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001922728.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001930124.1
Submitted: (Sep 23, 2021)
Evidence details

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs117692127...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021