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 in ESP (all): 39/13006=0.2%
ClinVar Genomic variation as it relates to human health
NM_015846.4(MBD1):c.1410G>A (p.Pro470=)
Germline
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.
(2)
Help
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.
Likely benign
2
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_015846.4(MBD1):c.1410G>A (p.Pro470=)
Variation ID: 403072 Accession: VCV000403072.6
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 18q21.1 18: 50273600 (GRCh38) [ NCBI UCSC ] 18: 47799970 (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 Apr 10, 2017 Oct 8, 2024 Mar 28, 2016 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_015846.4:c.1410G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_056671.2:p.Pro470= synonymous NM_001204136.2:c.1410G>A NP_001191065.1:p.Pro470= synonymous NM_001204137.2:c.1485G>A NP_001191066.1:p.Pro495= synonymous NM_001204138.2:c.1482G>A NP_001191067.1:p.Pro494= synonymous NM_001204139.2:c.1410G>A NP_001191068.1:p.Pro470= synonymous NM_001204140.2:c.1317G>A NP_001191069.1:p.Pro439= synonymous NM_001204141.2:c.1260G>A NP_001191070.1:p.Pro420= synonymous NM_001204142.2:c.1410G>A NP_001191071.1:p.Pro470= synonymous NM_001204143.2:c.1242G>A NP_001191072.1:p.Pro414= synonymous NM_001204151.3:c.1341G>A NP_001191080.1:p.Pro447= synonymous NM_001323942.1:c.1485G>A NM_001323942.2:c.1485G>A NP_001310871.1:p.Pro495= synonymous NM_001323947.2:c.1485G>A NP_001310876.1:p.Pro495= synonymous NM_001323949.2:c.978G>A NP_001310878.1:p.Pro326= synonymous NM_001323950.2:c.1407G>A NP_001310879.1:p.Pro469= synonymous NM_001323951.2:c.1410G>A NP_001310880.1:p.Pro470= synonymous NM_001323952.2:c.1167G>A NP_001310881.1:p.Pro389= synonymous NM_001323953.2:c.834G>A NP_001310882.1:p.Pro278= synonymous NM_001323954.2:c.1173G>A NP_001310883.1:p.Pro391= synonymous NM_001388138.1:c.1410G>A NP_001375067.1:p.Pro470= synonymous NM_001388139.1:c.1317G>A NP_001375068.1:p.Pro439= synonymous NM_001388140.1:c.1485G>A NP_001375069.1:p.Pro495= synonymous NM_001388141.1:c.1482G>A NP_001375070.1:p.Pro494= synonymous NM_001388142.1:c.1317G>A NP_001375071.1:p.Pro439= synonymous NM_001388143.1:c.1317G>A NP_001375072.1:p.Pro439= synonymous NM_001388144.1:c.1242G>A NP_001375073.1:p.Pro414= synonymous NM_001388145.1:c.1485G>A NP_001375074.1:p.Pro495= synonymous NM_001388146.1:c.1485G>A NP_001375075.1:p.Pro495= synonymous NM_001388147.1:c.1485G>A NP_001375076.1:p.Pro495= synonymous NM_001388148.1:c.1410G>A NP_001375077.1:p.Pro470= synonymous NM_001388149.1:c.1410G>A NP_001375078.1:p.Pro470= synonymous NM_001388150.1:c.1485G>A NP_001375079.1:p.Pro495= synonymous NM_001388151.1:c.1317G>A NP_001375080.1:p.Pro439= synonymous NM_001388152.1:c.1485G>A NP_001375081.1:p.Pro495= synonymous NM_001388153.1:c.1485G>A NP_001375082.1:p.Pro495= synonymous NM_001388154.1:c.1485G>A NP_001375083.1:p.Pro495= synonymous NM_001388155.1:c.1410G>A NP_001375084.1:p.Pro470= synonymous NM_001388156.1:c.1317G>A NP_001375085.1:p.Pro439= synonymous NM_001388157.1:c.1242G>A NP_001375086.1:p.Pro414= synonymous NM_001388158.1:c.1485G>A NP_001375087.1:p.Pro495= synonymous NM_001388159.1:c.1485G>A NP_001375088.1:p.Pro495= synonymous NM_001388160.1:c.1485G>A NP_001375089.1:p.Pro495= synonymous NM_001388161.1:c.1242G>A NP_001375090.1:p.Pro414= synonymous NM_001388162.1:c.1410G>A NP_001375091.1:p.Pro470= synonymous NM_001388163.1:c.1410G>A NP_001375092.1:p.Pro470= synonymous NM_001388164.1:c.1317G>A NP_001375093.1:p.Pro439= synonymous NM_001388165.1:c.1242G>A NP_001375094.1:p.Pro414= synonymous NM_001388166.1:c.1317G>A NP_001375095.1:p.Pro439= synonymous NM_001388167.1:c.1242G>A NP_001375096.1:p.Pro414= synonymous NM_002384.3:c.1242G>A NP_002375.1:p.Pro414= synonymous NM_015844.3:c.1242G>A NP_056669.2:p.Pro414= synonymous NM_015845.4:c.1341G>A NP_056670.2:p.Pro447= synonymous NM_015847.4:c.1263G>A NP_056723.2:p.Pro421= synonymous NC_000018.10:g.50273600C>T NC_000018.9:g.47799970C>T NG_029505.1:g.13175G>A - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000018.10:50273599:C:T
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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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0.00080 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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1000 Genomes Project 0.00080
1000 Genomes Project 30x 0.00094
Trans-Omics for Precision Medicine (TOPMed) 0.00210
The Genome Aggregation Database (gnomAD) 0.00267
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00300
Exome Aggregation Consortium (ExAC) 0.00343
- 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. |
|||
| MBD1 | - | - |
GRCh38 GRCh37 |
39 | 80 | |
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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
|
Mar 28, 2016 | RCV000455922.4 | |
|
MBD1-related disorder
|
Likely benign (1) |
no assertion criteria provided
|
Apr 11, 2019 | RCV003902631.2 |
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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Likely benign
(Mar 28, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000539592.1
First in ClinVar: Apr 10, 2017 Last updated: Apr 10, 2017 |
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 … (more)
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 in ESP (all): 39/13006=0.2% (less)
Method: Genome/Exome Filtration
|
|
|
Likely benign
(Apr 11, 2019)
|
no assertion criteria provided
Method: clinical testing
|
MBD1-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV004730737.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
|
Comment:
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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. |
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 in ESP (all): 39/13006=0.2%
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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 rs116701586 ...
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 Oct 13, 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.