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NM_000246.3(CIITA):c.384C>T (p.Ile128=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000317679.5
Variation ID:
317679
Description:
single nucleotide variant
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NM_000246.3(CIITA):c.384C>T (p.Ile128=)

Allele ID
323947
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.13
Genomic location
16: 10898950 (GRCh38) GRCh38 UCSC
16: 10992807 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.9:g.10992807C>T
NC_000016.10:g.10898950C>T
NM_001286402.1:c.387C>T NP_001273331.1:p.Ile129= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000016.10:10898949:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00006
1000 Genomes Project 0.00040
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA7899696
dbSNP: rs140106499
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 26, 2020 RCV000285263.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CIITA - - GRCh38
GRCh37
736 763

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Bare lymphocyte syndrome 2
Allele origin: germline
Invitae
Accession: SCV001051909.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Bare lymphocyte syndrome 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000394728.3
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)

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 rs140106499...

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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 Jun 06, 2021