NM_001378454.1(ALMS1):c.10440A>G (p.Ala3480=) AND Alstrom syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 2, 2024
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:: RCV001422832.8

Allele description [Variation Report for NM_001378454.1(ALMS1):c.10440A>G (p.Ala3480=)]

NM_001378454.1(ALMS1):c.10440A>G (p.Ala3480=)

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.10440A>G (p.Ala3480=)

HGVS:

NC_000002.12:g.73572317A>G
NG_011690.1:g.191565A>G
NM_001378454.1:c.10440A>GMANE SELECT
NM_015120.4:c.10443A>G
NP_001365383.1:p.Ala3480=
NP_055935.4:p.Ala3481=
LRG_741t1:c.10443A>G
LRG_741:g.191565A>G
LRG_741p1:p.Ala3481=
NC_000002.11:g.73799444A>G

Links:

dbSNP: rs375046790

NCBI 1000 Genomes Browser:

rs375046790

Molecular consequence:

NM_001378454.1:c.10440A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_015120.4:c.10443A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Alstrom syndrome (ALMS)
Synonyms:: Alstrom's syndrome
Identifiers:: MONDO: MONDO:0008763; MedGen: C0268425; Orphanet: 64; OMIM: 203800

Recent activity

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LOC401875 [Homo sapiens]
LOC401875 [Homo sapiens]
Gene ID:401875

Gene
related_functional_gene_54849[group] AND (alive[prop]) (1)
Gene
PREDICTED: Homo sapiens differentially expressed in FDCP 8 homolog (DEF8), trans...
PREDICTED: Homo sapiens differentially expressed in FDCP 8 homolog (DEF8), transcript variant X14, mRNA
gi|2217306435|ref|XM_017023364.3|

Nucleotide
Homo sapiens differentially expressed in FDCP 8 homolog (DEF8), transcript varia...
Homo sapiens differentially expressed in FDCP 8 homolog (DEF8), transcript variant 2, mRNA
gi|1677538139|ref|NM_017702.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001625390	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 2, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002794982	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 24, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001625390

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 2, 2024)

germline

clinical testing

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

SCV002794982

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Nov 24, 2021)

unknown

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001625390.4

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

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

From Fulgent Genetics, Fulgent Genetics, SCV002794982.1

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

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

Last Updated: Oct 20, 2024

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