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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ClinVar Genomic variation as it relates to human health
NM_000246.4(CIITA):c.2699A>G (p.Gln900Arg)
Germline
Classification
Help
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
Benign
5 out of 7 submissions contributed to this classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
7
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000246.4(CIITA):c.2699A>G (p.Gln900Arg)
Variation ID: 317718 Accession: VCV000317718.21
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 16p13.13 16: 10909070 (GRCh38) [ NCBI UCSC ] 16: 11002927 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 6, 2016 Apr 13, 2025 Feb 3, 2025 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000246.4:c.2699A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000237.2:p.Gln900Arg missense NM_001286402.1:c.2702A>G NP_001273331.1:p.Gln901Arg missense NM_001286403.2:c.947A>G NP_001273332.1:p.Gln316Arg missense NM_001379330.1:c.2555A>G NP_001366259.1:p.Gln852Arg missense NM_001379331.1:c.2552A>G NP_001366260.1:p.Gln851Arg missense NM_001379332.1:c.2702A>G NP_001366261.1:p.Gln901Arg missense NM_001379333.1:c.2699A>G NP_001366262.1:p.Gln900Arg missense NM_001379334.1:c.2630A>G NP_001366263.1:p.Gln877Arg missense NC_000016.10:g.10909070A>G NC_000016.9:g.11002927A>G NG_009628.1:g.36873A>G LRG_49:g.36873A>G LRG_49t1:c.2699A>G LRG_49p1:p.Gln900Arg - Protein change
- Q900R, Q316R, Q901R, Q851R, Q852R, Q877R
- Other names
- -
- Canonical SPDI
- NC_000016.10:10909069:A:G
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.07129 (A)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.91989
1000 Genomes Project 30x 0.92458
1000 Genomes Project 0.92871
The Genome Aggregation Database (gnomAD) 0.93380
Exome Aggregation Consortium (ExAC) 0.97872
The Genome Aggregation Database (gnomAD) 0.92908
The Genome Aggregation Database (gnomAD), exomes 0.98292
The Genome Aggregation Database (gnomAD), exomes 0.99366
Trans-Omics for Precision Medicine (TOPMed) 0.92455
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| CIITA | - | - |
GRCh38 GRCh37 |
1804 | 1880 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Benign (4) |
criteria provided, multiple submitters, no conflicts
|
Feb 3, 2025 | RCV000292677.17 | |
| Benign (1) |
criteria provided, single submitter
|
Mar 28, 2016 | RCV000455801.4 | |
| Benign (2) |
criteria provided, single submitter
|
- | RCV001824732.3 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Collapse all rows
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
|---|---|---|---|---|---|
|
Benign
(Jan 12, 2018)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
MHC class II deficiency 1 |
Illumina Laboratory Services, Illumina
Accession: SCV000394768.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
show
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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Benign
(Mar 28, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not specified |
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000538690.1
First in ClinVar: Apr 09, 2017 Last updated: Apr 09, 2017 |
Comment:
show
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Method: Genome/Exome Filtration
|
|
|
Benign
(Feb 03, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
MHC class II deficiency |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001727807.5
First in ClinVar: Jun 15, 2021 Last updated: Feb 25, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Benign
(Jul 10, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
MHC class II deficiency 1 |
Genome-Nilou Lab
Accession: SCV001761496.2
First in ClinVar: Jul 28, 2021 Last updated: Apr 13, 2025 |
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: no
Sex: mixed
|
|
|
Benign
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided
(Autosomal recessive inheritance)
|
Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005289597.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
Observation: 1
Collection method: not provided
Allele origin: germline
Affected status: yes
Observation 1
Collection method: not provided
Allele origin: germline
Affected status: yes
|
|
|
Benign
(Sep 16, 2020)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Bare lymphocyte syndrome type II |
Natera, Inc.
Accession: SCV001462356.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
not provided
(-)
N
Not contributing to aggregate classification
|
no classification provided
|
Not Provided |
GenomeConnect, ClinGen
Accession: SCV002074591.2
First in ClinVar: Feb 12, 2022 Last updated: Apr 13, 2025 |
Comment:
show
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. (less)
Observation: 1
Collection method: phenotyping only
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: phenotyping only
Allele origin: unknown
Affected status: unknown
Clinical Features:
Phenotypic abnormality (present)
Indication for testing: Diagnostic
Age: 40-49 years
Sex: female
Platform type: Gene Panel Sequencing
Testing laboratory: Labcorp Genetics (formerly Invitae), Labcorp
Date variant was reported to submitter: 2020-04-27
Testing laboratory interpretation: Benign
|
|
Comment:
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency
Comment:
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs7197779 ...
HelpThese 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 May 17, 2025
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.