NM_001378454.1(ALMS1):c.10628C>G (p.Thr3543Ser) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Feb 1, 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:: RCV000224685.9

Allele description [Variation Report for NM_001378454.1(ALMS1):c.10628C>G (p.Thr3543Ser)]

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

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.10628C>G (p.Thr3543Ser)

HGVS:

NC_000002.12:g.73572505C>G
NG_011690.1:g.191753C>G
NM_001378454.1:c.10628C>GMANE SELECT
NM_015120.4:c.10631C>G
NP_001365383.1:p.Thr3543Ser
NP_055935.4:p.Thr3544Ser
LRG_741t1:c.10631C>G
LRG_741:g.191753C>G
LRG_741p1:p.Thr3544Ser
NC_000002.11:g.73799632C>G
p.Thr3542Ser

Protein change:

T3543S

Links:

dbSNP: rs45501594

NCBI 1000 Genomes Browser:

rs45501594

Molecular consequence:

NM_001378454.1:c.10628C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015120.4:c.10631C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000280969	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Sep 29, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000531893	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jul 23, 2018)	germline	clinical testing	Citation Link,
SCV000840768	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Jul 31, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26239645, 26467025
SCV004155005	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Feb 1, 2024)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	13	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Rare coding variants and X-linked loci associated with age at menarche.

Lunetta KL, Day FR, Sulem P, Ruth KS, Tung JY, Hinds DA, Esko T, Elks CE, Altmaier E, He C, Huffman JE, Mihailov E, Porcu E, Robino A, Rose LM, Schick UM, Stolk L, Teumer A, Thompson DJ, Traglia M, Wang CA, Yerges-Armstrong LM, et al.

Nat Commun. 2015 Aug 4;6:7756. doi: 10.1038/ncomms8756. Erratum in: Nat Commun. 2015;6:10257.

PubMed [citation]

PMID:: 26239645
PMCID:: PMC4538850

See all PubMed Citations (3)

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000280969.1

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

Description

Converted during submission to Likely benign.

#	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		not provided	0.008408	not provided	not provided

From GeneDx, SCV000531893.4

#	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 associated with the following publications: (PMID: 26239645, 25846608)

#	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 Athena Diagnostics Inc, SCV000840768.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV004155005.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	13	not provided	not provided	clinical testing	not provided

Description

ALMS1: BP4, BS1, BS2

#	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		13	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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