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NM_015915.5(ATL1):c.669C>T (p.Tyr223=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Oct 1, 2021)
Last evaluated:
Apr 1, 2021
Accession:
VCV000313298.9
Variation ID:
313298
Description:
single nucleotide variant
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NM_015915.5(ATL1):c.669C>T (p.Tyr223=)

Allele ID
336046
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q22.1
Genomic location
14: 50613297 (GRCh38) GRCh38 UCSC
14: 51080015 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_360:g.85216C>T
LRG_360t2:c.669C>T LRG_360p2:p.Tyr223=
LRG_360t1:c.669C>T LRG_360p1:p.Tyr223=
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000014.9:50613296:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00077
The Genome Aggregation Database (gnomAD), exomes 0.00081
The Genome Aggregation Database (gnomAD) 0.00059
Exome Aggregation Consortium (ExAC) 0.00079
The Genome Aggregation Database (gnomAD) 0.00045
Trans-Omics for Precision Medicine (TOPMed) 0.00057
Trans-Omics for Precision Medicine (TOPMed) 0.00060
Links
ClinGen: CA7180315
dbSNP: rs146975855
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 12, 2020 RCV000471358.7
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Apr 1, 2021 RCV001531188.2
Benign 1 criteria provided, single submitter Jun 28, 2017 RCV000427052.4
Likely benign 1 criteria provided, single submitter Dec 9, 2019 RCV001286239.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATL1 - - GRCh38
GRCh37
281 310

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jun 28, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612431.1
Submitted: (Aug 17, 2017)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000386889.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Nov 12, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Allele origin: germline
Invitae
Accession: SCV000561597.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 18, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000518502.5
Submitted: (Oct 01, 2021)
Evidence details
Likely benign
(Dec 09, 2019)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001472774.1
Submitted: (Dec 11, 2020)
Evidence details
Likely benign
(Apr 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001746192.1
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs146975855...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021