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NM_004646.4(NPHS1):c.1638T>G (p.Thr546=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Oct 22, 2021)
Last evaluated:
Jan 19, 2021
Accession:
VCV000328869.8
Variation ID:
328869
Description:
single nucleotide variant
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NM_004646.4(NPHS1):c.1638T>G (p.Thr546=)

Allele ID
343280
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19q13.12
Genomic location
19: 35845788 (GRCh38) GRCh38 UCSC
19: 36336690 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_693:g.28500T>G
LRG_693t1:c.1638T>G LRG_693p1:p.Thr546=
NC_000019.10:g.35845788A>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:35845787:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00166
The Genome Aggregation Database (gnomAD), exomes 0.00167
Trans-Omics for Precision Medicine (TOPMed) 0.00167
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00215
1000 Genomes Project 0.00060
Exome Aggregation Consortium (ExAC) 0.00164
Links
ClinGen: CA9390367
dbSNP: rs115444936
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Jan 19, 2021 RCV000588114.6
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000366917.2
Likely benign 1 no assertion criteria provided Nov 11, 2019 RCV001277291.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NPHS1 - - GRCh38
GRCh37
755 805

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Congenital nephrotic syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000411572.3
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
(Oct 17, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000698498.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The NPHS1 c.1638T>G (p.Thr546Thr) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predict no significant impact on … (more)
Benign
(Jan 15, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000842913.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001096571.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 19, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001981892.1
Submitted: (Oct 22, 2021)
Evidence details
Likely benign
(Nov 11, 2019)
no assertion criteria provided
Method: clinical testing
Finnish congenital nephrotic syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001464213.1
Submitted: (Dec 28, 2020)
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 rs115444936...

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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 Nov 20, 2021