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NM_001378454.1(ALMS1):c.12108C>G (p.Thr4036=) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 4, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000424951.1

Allele description [Variation Report for NM_001378454.1(ALMS1):c.12108C>G (p.Thr4036=)]

NM_001378454.1(ALMS1):c.12108C>G (p.Thr4036=)

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.12108C>G (p.Thr4036=)
HGVS:
  • NC_000002.12:g.73601430C>G
  • NG_011690.1:g.220678C>G
  • NM_001378454.1:c.12108C>GMANE SELECT
  • NM_015120.4:c.12111C>G
  • NP_001365383.1:p.Thr4036=
  • NP_055935.4:p.Thr4037=
  • LRG_741t1:c.12111C>G
  • LRG_741:g.220678C>G
  • LRG_741p1:p.Thr4037=
  • NC_000002.11:g.73828557C>G
Links:
dbSNP: rs767174517
NCBI 1000 Genomes Browser:
rs767174517
Molecular consequence:
  • NM_001378454.1:c.12108C>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_015120.4:c.12111C>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000533458GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Nov 4, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000533458.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Although the c.12111 C>G variant is a synonymous change, one splicing algorithm suggests that this nucleotide substitution destroys the natural splice donor site in intron 19, and may lead to abnormal splicing. The c.12111 C>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.12111 C>G variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. Nonetheless, two other splicing algorithims predict no effect to the natural splice donor site in intron 19. Furthermore, this nucletotide substitution is not conserved across species. Segregation and functional mRNA studies are necessary to clarify the role of this variant in disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024