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NM_001089.3(ABCA3):c.5101G>A (p.Glu1701Lys)

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Interpretation:
Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jul 31, 2019)
Last evaluated:
Jul 6, 2019
Accession:
VCV000227154.3
Variation ID:
227154
Description:
single nucleotide variant
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NM_001089.3(ABCA3):c.5101G>A (p.Glu1701Lys)

Allele ID
230624
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2276688 (GRCh38) GRCh38 UCSC
16: 2326689 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.2276688C>T
NC_000016.9:g.2326689C>T
NM_001089.3:c.5101G>A MANE Select NP_001080.2:p.Glu1701Lys missense
NG_011790.1:g.69059G>A
Protein change
E1701K
Other names
-
Canonical SPDI
NC_000016.10:2276687:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00219
The Genome Aggregation Database (gnomAD) 0.00188
1000 Genomes Project 0.00200
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00254
Links
dbSNP: rs139954112
ClinGen: CA7839895
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jan 14, 2016 RCV000216001.1
Likely benign 1 criteria provided, single submitter Jul 6, 2019 RCV000853222.1
Likely benign 1 criteria provided, single submitter Jul 23, 2018 RCV000965316.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ABCA3 - - GRCh38
GRCh37
364 402

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 14, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000269960.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Glu1701Lys in exon 33 of ABCA3: This variant is not expected to have clinical significance because it has been identified in 0.7% (72/10220) of African … (more)
Likely benign
(Jul 06, 2019)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV000996034.1
Submitted: (Jul 31, 2019)
Evidence details
Likely benign
(Jul 23, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001112581.1
Submitted: (Mar 14, 2019)
Evidence details

Functional evidence

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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

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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 rs139954112...

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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 Jul 07, 2021