NM_001048166.1(STIL):c.1455G>C (p.Leu485Phe) AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Mar 21, 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:: RCV000174311.15

Allele description [Variation Report for NM_001048166.1(STIL):c.1455G>C (p.Leu485Phe)]

NM_001048166.1(STIL):c.1455G>C (p.Leu485Phe)

Gene:

STIL:STIL centriolar assembly protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p33

Genomic location:

Preferred name:

NM_001048166.1(STIL):c.1455G>C (p.Leu485Phe)

HGVS:

NC_000001.11:g.47281003C>G
NG_012126.1:g.38145G>C
NM_001048166.1:c.1455G>CMANE SELECT
NM_001282936.1:c.1455G>C
NM_001282937.1:c.1455G>C
NM_001282938.1:c.1314G>C
NM_001282939.1:c.1314G>C
NM_003035.2:c.1455G>C
NP_001041631.1:p.Leu485Phe
NP_001269865.1:p.Leu485Phe
NP_001269866.1:p.Leu485Phe
NP_001269867.1:p.Leu438Phe
NP_001269868.1:p.Leu438Phe
NP_003026.2:p.Leu485Phe
NC_000001.10:g.47746675C>G

Protein change:

L438F

Links:

dbSNP: rs139912214

NCBI 1000 Genomes Browser:

rs139912214

Molecular consequence:

NM_001048166.1:c.1455G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282936.1:c.1455G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282937.1:c.1455G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282938.1:c.1314G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282939.1:c.1314G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003035.2:c.1455G>C - 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
SCV000195133	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 26, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000225592	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely benign (Aug 19, 2015)	germline	clinical testing	Citation Link,
SCV000519711	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Feb 2, 2018)	germline	clinical testing	Citation Link,
SCV004847465	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Mar 21, 2024)	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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	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

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000195133.2

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000225592.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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	unknown	not provided	not provided	not provided		3	not provided	not provided	not provided

From GeneDx, SCV000519711.4

#	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, SCV004847465.1

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

Description

The p.Leu438Phe variant in STIL is classified as likely benign because it has been identified in 0.9% (267/29604) of Ashkenazi Jewish chromosomes, 0.4% (29/6060) of Middle Eastern chromosomes and 0.3% (156/60012) of Admixed American chromosomes, including 6 total homozygotes by gnomAD (http://gnomad.broadinstitute.org, v.4.0.0). In addition, computational prediction tools predict that this variant does not impact the protein. ACMG/AMP Criteria applied: BS1, BP4.

#	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: Jun 17, 2024

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