ClinVar Genomic variation as it relates to human health
NM_001405607.1(PBRM1):c.1479C>T (p.Ile493=)
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.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001405607.1(PBRM1):c.1479C>T (p.Ile493=)
Variation ID: 770703 Accession: VCV000770703.11
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p21.1 3: 52627335 (GRCh38) [ NCBI UCSC ] 3: 52661351 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 17, 2019 Aug 4, 2024 Jul 1, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001405607.1:c.1479C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001392536.1:p.Ile493= synonymous NM_001350074.2:c.1542C>T NP_001337003.1:p.Ile514= synonymous NM_001350075.2:c.1479C>T NP_001337004.1:p.Ile493= synonymous NM_001350076.2:c.1542C>T NP_001337005.1:p.Ile514= synonymous NM_001350077.2:c.1533C>T NP_001337006.1:p.Ile511= synonymous NM_001350078.2:c.1542C>T NP_001337007.1:p.Ile514= synonymous NM_001350079.2:c.1542C>T NP_001337008.1:p.Ile514= synonymous NM_001366070.2:c.1542C>T NP_001352999.1:p.Ile514= synonymous NM_001366071.2:c.1542C>T NP_001353000.1:p.Ile514= synonymous NM_001366072.2:c.1542C>T NP_001353001.1:p.Ile514= synonymous NM_001366073.2:c.1533C>T NP_001353002.1:p.Ile511= synonymous NM_001366074.2:c.1530C>T NP_001353003.1:p.Ile510= synonymous NM_001366075.2:c.1542C>T NP_001353004.1:p.Ile514= synonymous NM_001366076.2:c.1437C>T NP_001353005.1:p.Ile479= synonymous NM_001394867.1:c.1479C>T NP_001381796.1:p.Ile493= synonymous NM_001394868.1:c.1479C>T NP_001381797.1:p.Ile493= synonymous NM_001394869.1:c.1479C>T NP_001381798.1:p.Ile493= synonymous NM_001394870.1:c.1533C>T NP_001381799.1:p.Ile511= synonymous NM_001394871.1:c.1479C>T NP_001381800.1:p.Ile493= synonymous NM_001394872.1:c.1479C>T NP_001381801.1:p.Ile493= synonymous NM_001394873.1:c.1479C>T NP_001381802.1:p.Ile493= synonymous NM_001394874.1:c.1479C>T NP_001381803.1:p.Ile493= synonymous NM_001394875.1:c.1479C>T NP_001381804.1:p.Ile493= synonymous NM_001394876.1:c.1479C>T NP_001381805.1:p.Ile493= synonymous NM_001394877.1:c.1479C>T NP_001381806.1:p.Ile493= synonymous NM_001394878.1:c.1443C>T NP_001381807.1:p.Ile481= synonymous NM_001394879.1:c.1383C>T NP_001381808.1:p.Ile461= synonymous NM_001400470.1:c.1479C>T NP_001387399.1:p.Ile493= synonymous NM_001400471.1:c.1479C>T NP_001387400.1:p.Ile493= synonymous NM_001400472.1:c.1500C>T NP_001387401.1:p.Ile500= synonymous NM_001400473.1:c.1479C>T NP_001387402.1:p.Ile493= synonymous NM_001400474.1:c.1479C>T NP_001387403.1:p.Ile493= synonymous NM_001400475.1:c.1479C>T NP_001387404.1:p.Ile493= synonymous NM_001400479.1:c.1479C>T NP_001387408.1:p.Ile493= synonymous NM_001400481.1:c.1479C>T NP_001387410.1:p.Ile493= synonymous NM_001400484.1:c.1479C>T NP_001387413.1:p.Ile493= synonymous NM_001400487.1:c.1383C>T NP_001387416.1:p.Ile461= synonymous NM_001400490.1:c.1479C>T NP_001387419.1:p.Ile493= synonymous NM_001400496.1:c.1479C>T NP_001387425.1:p.Ile493= synonymous NM_001400500.1:c.1479C>T NP_001387429.1:p.Ile493= synonymous NM_001400501.1:c.1479C>T NP_001387430.1:p.Ile493= synonymous NM_001400504.1:c.1479C>T NP_001387433.1:p.Ile493= synonymous NM_001405552.1:c.1581C>T NP_001392481.1:p.Ile527= synonymous NM_001405553.1:c.1542C>T NP_001392482.1:p.Ile514= synonymous NM_001405554.1:c.1587C>T NP_001392483.1:p.Ile529= synonymous NM_001405555.1:c.1479C>T NP_001392484.1:p.Ile493= synonymous NM_001405556.1:c.1479C>T NP_001392485.1:p.Ile493= synonymous NM_001405557.1:c.1479C>T NP_001392486.1:p.Ile493= synonymous NM_001405558.1:c.1479C>T NP_001392487.1:p.Ile493= synonymous NM_001405559.1:c.1479C>T NP_001392488.1:p.Ile493= synonymous NM_001405560.1:c.1380C>T NP_001392489.1:p.Ile460= synonymous NM_001405561.1:c.1479C>T NP_001392490.1:p.Ile493= synonymous NM_001405563.1:c.1479C>T NP_001392492.1:p.Ile493= synonymous NM_001405564.1:c.1506C>T NP_001392493.1:p.Ile502= synonymous NM_001405565.1:c.1479C>T NP_001392494.1:p.Ile493= synonymous NM_001405566.1:c.-504C>T 5 prime UTR NM_001405567.1:c.1479C>T NP_001392496.1:p.Ile493= synonymous NM_001405568.1:c.1506C>T NP_001392497.1:p.Ile502= synonymous NM_001405569.1:c.1506C>T NP_001392498.1:p.Ile502= synonymous NM_001405570.1:c.1479C>T NP_001392499.1:p.Ile493= synonymous NM_001405571.1:c.1479C>T NP_001392500.1:p.Ile493= synonymous NM_001405572.1:c.1383C>T NP_001392501.1:p.Ile461= synonymous NM_001405573.1:c.1293C>T NP_001392502.1:p.Ile431= synonymous NM_001405574.1:c.1533C>T NP_001392503.1:p.Ile511= synonymous NM_001405575.1:c.1479C>T NP_001392504.1:p.Ile493= synonymous NM_001405576.1:c.1479C>T NP_001392505.1:p.Ile493= synonymous NM_001405577.1:c.1479C>T NP_001392506.1:p.Ile493= synonymous NM_001405578.1:c.1479C>T NP_001392507.1:p.Ile493= synonymous NM_001405579.1:c.1479C>T NP_001392508.1:p.Ile493= synonymous NM_001405580.1:c.1506C>T NP_001392509.1:p.Ile502= synonymous NM_001405581.1:c.1479C>T NP_001392510.1:p.Ile493= synonymous NM_001405582.1:c.1383C>T NP_001392511.1:p.Ile461= synonymous NM_001405583.1:c.1479C>T NP_001392512.1:p.Ile493= synonymous NM_001405584.1:c.1479C>T NP_001392513.1:p.Ile493= synonymous NM_001405585.1:c.1479C>T NP_001392514.1:p.Ile493= synonymous NM_001405586.1:c.1506C>T NP_001392515.1:p.Ile502= synonymous NM_001405587.1:c.1335C>T NP_001392516.1:p.Ile445= synonymous NM_001405588.1:c.1479C>T NP_001392517.1:p.Ile493= synonymous NM_001405589.1:c.1479C>T NP_001392518.1:p.Ile493= synonymous NM_001405590.1:c.1479C>T NP_001392519.1:p.Ile493= synonymous NM_001405591.1:c.1533C>T NP_001392520.1:p.Ile511= synonymous NM_001405592.1:c.1479C>T NP_001392521.1:p.Ile493= synonymous NM_001405593.1:c.1479C>T NP_001392522.1:p.Ile493= synonymous NM_001405594.1:c.1479C>T NP_001392523.1:p.Ile493= synonymous NM_001405595.1:c.1410C>T NP_001392524.1:p.Ile470= synonymous NM_001405596.1:c.-504C>T 5 prime UTR NM_001405597.1:c.1362C>T NP_001392526.1:p.Ile454= synonymous NM_001405598.1:c.1506C>T NP_001392527.1:p.Ile502= synonymous NM_001405599.1:c.1383C>T NP_001392528.1:p.Ile461= synonymous NM_001405600.1:c.1533C>T NP_001392529.1:p.Ile511= synonymous NM_001405601.1:c.1479C>T NP_001392530.1:p.Ile493= synonymous NM_001405602.1:c.1383C>T NP_001392531.1:p.Ile461= synonymous NM_001405603.1:c.1479C>T NP_001392532.1:p.Ile493= synonymous NM_001405604.1:c.1383C>T NP_001392533.1:p.Ile461= synonymous NM_001405605.1:c.1479C>T NP_001392534.1:p.Ile493= synonymous NM_001405606.1:c.1383C>T NP_001392535.1:p.Ile461= synonymous NM_001405608.1:c.342C>T NP_001392537.1:p.Ile114= synonymous NM_001405609.1:c.1479C>T NP_001392538.1:p.Ile493= synonymous NM_001405610.1:c.1479C>T NP_001392539.1:p.Ile493= synonymous NM_001405611.1:c.1479C>T NP_001392540.1:p.Ile493= synonymous NM_001405612.1:c.1479C>T NP_001392541.1:p.Ile493= synonymous NM_001405622.1:c.1542C>T NP_001392551.1:p.Ile514= synonymous NM_001405623.1:c.1479C>T NP_001392552.1:p.Ile493= synonymous NM_001405624.1:c.1479C>T NP_001392553.1:p.Ile493= synonymous NM_001405625.1:c.-104C>T 5 prime UTR NM_001405626.1:c.1479C>T NP_001392555.1:p.Ile493= synonymous NM_001405627.1:c.1479C>T NP_001392556.1:p.Ile493= synonymous NM_001405628.1:c.1479C>T NP_001392557.1:p.Ile493= synonymous NM_001405629.1:c.1479C>T NP_001392558.1:p.Ile493= synonymous NM_001405630.1:c.1479C>T NP_001392559.1:p.Ile493= synonymous NM_001405631.1:c.1479C>T NP_001392560.1:p.Ile493= synonymous NM_001405632.1:c.1479C>T NP_001392561.1:p.Ile493= synonymous NM_001405633.1:c.1479C>T NP_001392562.1:p.Ile493= synonymous NM_001405634.1:c.1479C>T NP_001392563.1:p.Ile493= synonymous NM_001405635.1:c.1479C>T NP_001392564.1:p.Ile493= synonymous NM_001405636.1:c.1506C>T NP_001392565.1:p.Ile502= synonymous NM_001405637.1:c.1497C>T NP_001392566.1:p.Ile499= synonymous NM_001405638.1:c.1383C>T NP_001392567.1:p.Ile461= synonymous NM_001405639.1:c.1479C>T NP_001392568.1:p.Ile493= synonymous NM_001405640.1:c.1479C>T NP_001392569.1:p.Ile493= synonymous NM_001405641.1:c.1479C>T NP_001392570.1:p.Ile493= synonymous NM_001405642.1:c.1380C>T NP_001392571.1:p.Ile460= synonymous NM_001405643.1:c.1479C>T NP_001392572.1:p.Ile493= synonymous NM_018165.4:c.1383C>T NP_060635.2:p.Ile461= synonymous NM_018313.5:c.1479C>T NP_060783.3:p.Ile493= synonymous NM_181042.5:c.1479C>T NP_851385.1:p.Ile493= synonymous NR_174502.1:n.1659C>T non-coding transcript variant NR_175959.1:n.1656C>T non-coding transcript variant NC_000003.12:g.52627335G>A NC_000003.11:g.52661351G>A NG_032108.1:g.63516C>T - Protein change
- Other names
- -
- Canonical SPDI
- NC_000003.12:52627334:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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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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0.00260 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.00234
1000 Genomes Project 0.00260
The Genome Aggregation Database (gnomAD), exomes 0.00468
Exome Aggregation Consortium (ExAC) 0.00479
Trans-Omics for Precision Medicine (TOPMed) 0.00517
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00700
- 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 | ||
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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. |
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PBRM1 | - | - |
GRCh38 GRCh37 |
65 | 76 |
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. |
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Benign/Likely benign (2) |
criteria provided, multiple submitters, no conflicts
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Jul 1, 2023 | RCV000949897.11 |
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. |
More information
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. |
|
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Benign
(May 25, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001096171.1
First in ClinVar: Dec 17, 2019 Last updated: Dec 17, 2019 |
|
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Likely benign
(Jul 01, 2023)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004150329.8
First in ClinVar: Nov 20, 2023 Last updated: Aug 04, 2024 |
Comment:
PBRM1: BP4, BP7, BS2
Number of individuals with the variant: 2
|
Germline Functional Evidence
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 germline classification of this variant
HelpThere 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 rs147488144 ...
HelpRecord last updated Aug 04, 2024
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.