NM_001378454.1(ALMS1):c.12114+12T>C AND Alstrom syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Dec 1, 2023
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:: RCV000667201.7

Allele description [Variation Report for NM_001378454.1(ALMS1):c.12114+12T>C]

NM_001378454.1(ALMS1):c.12114+12T>C

Genes:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]
LOC126806252:BRD4-independent group 4 enhancer GRCh37_chr2:73828496-73829695 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.1

Genomic location:

Preferred name:

NM_001378454.1(ALMS1):c.12114+12T>C

HGVS:

NC_000002.12:g.73601448T>C
NG_011690.1:g.220696T>C
NM_001378454.1:c.12114+12T>CMANE SELECT
NM_015120.4:c.12114+12T>C
LRG_741t1:c.12114+12T>C
LRG_741:g.220696T>C
NC_000002.11:g.73828575T>C
NM_015120.4:c.12117+12T>C

Links:

dbSNP: rs377393930

NCBI 1000 Genomes Browser:

rs377393930

Molecular consequence:

NM_001378454.1:c.12114+12T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_015120.4:c.12114+12T>C - intron variant - [Sequence Ontology: SO:0001627]

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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phospholipid-transporting ATPase 2 [Momordica charantia]
phospholipid-transporting ATPase 2 [Momordica charantia]
gi|1229789014|ref|XP_022147926.1|

Protein
phospholipid-transporting ATPase 2-like [Cucurbita moschata]
phospholipid-transporting ATPase 2-like [Cucurbita moschata]
gi|1279840666|ref|XP_022930833.1|

Protein
PREDICTED: probable mediator of RNA polymerase II transcription subunit 26b [Cuc...
PREDICTED: probable mediator of RNA polymerase II transcription subunit 26b [Cucumis melo]
gi|659085053|ref|XP_008443218.1|

Protein
putative protein phosphatase 2C 60, partial [Cucurbita argyrosperma subsp. soror...
putative protein phosphatase 2C 60, partial [Cucurbita argyrosperma subsp. sororia]
gi|2047933619|gb|KAG6603887.1||gnl| AGKQH|SDJN03_04496

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000791619	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely benign (Jul 20, 2017)	unknown	clinical testing	Citation Link,
SCV002469973	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 1, 2023)	germline	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

SCV000791619

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely benign
(Jul 20, 2017)

unknown

clinical testing

Citation Link,

SCV002469973

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 1, 2023)

germline

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

Details of each submission

From Counsyl, SCV000791619.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002469973.3

#	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

Last Updated: Sep 29, 2024

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