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_001963.6(EGF):c.1602G>A (p.Lys534=)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000778314.5
Variation ID:
778314
Description:
single nucleotide variant
Help

NM_001963.6(EGF):c.1602G>A (p.Lys534=)

Allele ID
698335
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4q25
Genomic location
4: 109968997 (GRCh38) GRCh38 UCSC
4: 110890153 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.110890153G>A
NC_000004.12:g.109968997G>A
NG_011441.1:g.61114G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000004.12:109968996:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00160 (A)

Allele frequency
1000 Genomes Project 0.00160
The Genome Aggregation Database (gnomAD) 0.00197
Trans-Omics for Precision Medicine (TOPMed) 0.00208
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00223
Exome Aggregation Consortium (ExAC) 0.00172
The Genome Aggregation Database (gnomAD), exomes 0.00185
Links
dbSNP: rs140682556
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, single submitter Dec 31, 2019 RCV000958935.4
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001151103.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EGF - - GRCh38
GRCh37
240 251

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001105820.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hypomagnesemia 4, renal
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001312206.1
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
(-)
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: SCV001928126.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001971777.1
Submitted: (Sep 21, 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 rs140682556...

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 Oct 07, 2021