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NM_001378454.1(ALMS1):c.10628C>G (p.Thr3543Ser)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 25, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000221028.7
Variation ID:
221028
Description:
single nucleotide variant
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NM_001378454.1(ALMS1):c.10628C>G (p.Thr3543Ser)

Allele ID
221338
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p13.1
Genomic location
2: 73572505 (GRCh38) GRCh38 UCSC
2: 73799632 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.73799632C>G
NC_000002.12:g.73572505C>G
NG_011690.1:g.191753C>G
... more HGVS
Protein change
T3544S, T3543S
Other names
-
Canonical SPDI
NC_000002.12:73572504:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (G)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00624
Exome Aggregation Consortium (ExAC) 0.00690
Trans-Omics for Precision Medicine (TOPMed) 0.00693
1000 Genomes Project 0.00180
The Genome Aggregation Database (gnomAD), exomes 0.00664
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00903
The Genome Aggregation Database (gnomAD) 0.00688
Trans-Omics for Precision Medicine (TOPMed) 0.00717
Links
ClinGen: CA349169
dbSNP: rs45501594
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 3 criteria provided, multiple submitters, no conflicts Jul 31, 2018 RCV000224685.5
Benign 3 criteria provided, multiple submitters, no conflicts Dec 14, 2017 RCV000434829.5
Benign 1 criteria provided, single submitter Feb 1, 2019 RCV000445553.3
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV001079318.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ALMS1 - - GRCh38
GRCh37
2486 2498

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely Benign
(Sep 29, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000280969.1
Submitted: (May 19, 2016)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(Jul 31, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000840768.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Benign
(Jan 25, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000705014.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Aug 02, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000864099.1
Submitted: (Dec 12, 2018)
Evidence details
Comment:
Variant summary: The ALMS1 c.10625C>G (p.Thr3542Ser, alternative name c.10631C>G) variant involves the alteration of a non-conserved nucleotide. 4/5 in silico tools predict a benign outcome … (more)
Benign
(Dec 14, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000711946.1
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Thr3542Ser in exon 16 of ALMS1: This variant is not expected to have clinical significance because it has been identified in 1.03% (1297/125086) of European … (more)
Benign
(Feb 01, 2019)
criteria provided, single submitter
Method: research
Monogenic diabetes
Allele origin: unknown
Personalized Diabetes Medicine Program,University of Maryland School of Medicine
Accession: SCV000536990.2
Submitted: (Feb 19, 2020)
Evidence details
Comment:
ACMG criteria: BP4 (six predictors plus Revel score: 0.024; not using PP3's three predictors), BA1 (1% in gnomAD European population), BS2 (15 homozygotes in gnomAD), … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Alstrom syndrome
Allele origin: germline
Invitae
Accession: SCV000262122.8
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 23, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000531893.4
Submitted: (Sep 25, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 26239645, 25846608)

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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Title Author Journal Year Link
Rare coding variants and X-linked loci associated with age at menarche. Lunetta KL Nature communications 2015 PMID: 26239645
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ALMS1 - - - -

Text-mined citations for rs45501594...

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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 27, 2021