NM_001378454.1(ALMS1):c.4154C>G (p.Thr1385Arg) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Oct 11, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000418663.7

Allele description [Variation Report for NM_001378454.1(ALMS1):c.4154C>G (p.Thr1385Arg)]

NM_001378454.1(ALMS1):c.4154C>G (p.Thr1385Arg)

Gene:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.1

Genomic location:

Preferred name:

NM_001378454.1(ALMS1):c.4154C>G (p.Thr1385Arg)

HGVS:

NC_000002.12:g.73450681C>G
NG_011690.1:g.69929C>G
NM_001378454.1:c.4154C>GMANE SELECT
NM_015120.4:c.4157C>G
NP_001365383.1:p.Thr1385Arg
NP_055935.4:p.Thr1386Arg
LRG_741t1:c.4157C>G
LRG_741:g.69929C>G
LRG_741p1:p.Thr1386Arg
NC_000002.11:g.73677808C>G

Protein change:

T1385R

Links:

dbSNP: rs115517108

NCBI 1000 Genomes Browser:

rs115517108

Molecular consequence:

NM_001378454.1:c.4154C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015120.4:c.4157C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000529347	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Oct 11, 2016)	germline	clinical testing	Citation Link,
SCV000966251	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Mar 21, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002034245	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000529347

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Oct 11, 2016)

germline

clinical testing

Citation Link,

SCV000966251

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Mar 21, 2016)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002034245

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Benign

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	4	4	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From GeneDx, SCV000529347.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000966251.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	PubMed (1)

Description

p.Thr1384Arg in exon 8 of ALMS1: This variant is not expected to have clinical s ignificance because it has been identified in 5.85% (573/9792) of African chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs115517108).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		4	not provided	4	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV002034245.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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