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NM_015915.5(ATL1):c.84A>G (p.Pro28=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000021534.9
Variation ID:
21534
Description:
single nucleotide variant
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NM_015915.5(ATL1):c.84A>G (p.Pro28=)

Allele ID
34386
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q22.1
Genomic location
14: 50587880 (GRCh38) GRCh38 UCSC
14: 51054598 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_360:g.59799A>G
LRG_360t2:c.84A>G LRG_360p2:p.Pro28=
LRG_360t1:c.84A>G LRG_360p1:p.Pro28=
... more HGVS
Protein change
-
Other names
p.P28P:CCA>CCG
Canonical SPDI
NC_000014.9:50587879:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.16414 (G)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.17994
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.20145
Trans-Omics for Precision Medicine (TOPMed) 0.18664
The Genome Aggregation Database (gnomAD) 0.18809
Exome Aggregation Consortium (ExAC) 0.13591
The Genome Aggregation Database (gnomAD), exomes 0.13112
1000 Genomes Project 0.16414
Trans-Omics for Precision Medicine (TOPMed) 0.18461
Links
ClinGen: CA151914
dbSNP: rs35014209
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Dec 3, 2020 RCV000020724.5
Benign 4 criteria provided, single submitter Dec 30, 2013 RCV000116421.8
Benign 1 criteria provided, single submitter Apr 30, 2017 RCV000576658.1
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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
(Dec 30, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167051.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Benign
(Apr 30, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Hereditary sensory neuropathy type 1D
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000677511.1
Submitted: (Jul 17, 2017)
Evidence details
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000386879.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Allele origin: germline
Invitae
Accession: SCV001000491.3
Submitted: (Jan 07, 2021)
Evidence details
benign
(Sep 21, 2010)
no assertion criteria provided
Method: curation
Spastic Paraplegia 3A
Allele origin: not provided
GeneReviews
Accession: SCV000041297.1
Submitted: (Jan 08, 2013)
Evidence details
Comment:
Converted during submission to Benign.
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000150346.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001918139.1
Submitted: (Sep 23, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959045.1
Submitted: (Sep 30, 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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Title Author Journal Year Link
Spastic Paraplegia 3A Hedera P - 2020 PMID: 20862796

Text-mined citations for rs35014209...

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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