The c.1961C>T (p.T654M) alteration is located in exon 22 (coding exon 15) of the NBPF15 gene. This alteration results from a C to T substitution at nucleotide position 1961, causing the threonine (T) at amino acid position 654 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_001385408.1(NBPF15):c.1961C>T (p.Thr654Met)
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.
(1)
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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001385408.1(NBPF15):c.1961C>T (p.Thr654Met)
Variation ID: 3298645 Accession: VCV003298645.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q21.1 1: 144423065 (GRCh38) [ NCBI UCSC ] 1: 148594588 (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 Aug 11, 2024 Aug 11, 2024 May 26, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001385408.1:c.1961C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001372337.1:p.Thr654Met missense NM_001170755.3:c.1961C>T NP_001164226.1:p.Thr654Met missense NM_001385373.1:c.1961C>T NP_001372302.1:p.Thr654Met missense NM_001385374.1:c.1961C>T NP_001372303.1:p.Thr654Met missense NM_001385375.1:c.1961C>T NP_001372304.1:p.Thr654Met missense NM_001385376.1:c.1961C>T NP_001372305.1:p.Thr654Met missense NM_001385377.1:c.1961C>T NP_001372306.1:p.Thr654Met missense NM_001385378.1:c.1961C>T NP_001372307.1:p.Thr654Met missense NM_001385403.1:c.1961C>T NP_001372332.1:p.Thr654Met missense NM_001385404.1:c.1961C>T NP_001372333.1:p.Thr654Met missense NM_001385405.1:c.1961C>T NP_001372334.1:p.Thr654Met missense NM_001385406.1:c.1961C>T NP_001372335.1:p.Thr654Met missense NM_001385407.1:c.1961C>T NP_001372336.1:p.Thr654Met missense NM_001385409.1:c.1961C>T NP_001372338.1:p.Thr654Met missense NM_001385410.1:c.1961C>T NP_001372339.1:p.Thr654Met missense NM_001385411.1:c.1961C>T NP_001372340.1:p.Thr654Met missense NM_001385412.1:c.1961C>T NP_001372341.1:p.Thr654Met missense NM_001385413.1:c.1961C>T NP_001372342.1:p.Thr654Met missense NM_001385414.1:c.1961C>T NP_001372343.1:p.Thr654Met missense NM_001385415.1:c.1961C>T NP_001372344.1:p.Thr654Met missense NM_001385416.1:c.1961C>T NP_001372345.1:p.Thr654Met missense NM_001385417.1:c.1961C>T NP_001372346.1:p.Thr654Met missense NM_001385418.1:c.1961C>T NP_001372347.1:p.Thr654Met missense NM_001385419.1:c.1961C>T NP_001372348.1:p.Thr654Met missense NM_001385420.1:c.1961C>T NP_001372349.1:p.Thr654Met missense NM_001385421.1:c.1961C>T NP_001372350.1:p.Thr654Met missense NM_001385422.1:c.1961C>T NP_001372351.1:p.Thr654Met missense NM_001385423.1:c.1961C>T NP_001372352.1:p.Thr654Met missense NM_001385424.1:c.1961C>T NP_001372353.1:p.Thr654Met missense NM_001385425.1:c.1961C>T NP_001372354.1:p.Thr654Met missense NM_001385426.1:c.1961C>T NP_001372355.1:p.Thr654Met missense NM_001385427.1:c.1961C>T NP_001372356.1:p.Thr654Met missense NM_001385428.1:c.1961C>T NP_001372357.1:p.Thr654Met missense NM_001385429.1:c.1961C>T NP_001372358.1:p.Thr654Met missense NM_001385430.1:c.1961C>T NP_001372359.1:p.Thr654Met missense NM_001385431.1:c.1961C>T NP_001372360.1:p.Thr654Met missense NM_001385432.1:c.1961C>T NP_001372361.1:p.Thr654Met missense NM_001385433.1:c.1961C>T NP_001372362.1:p.Thr654Met missense NM_001385434.1:c.1961C>T NP_001372363.1:p.Thr654Met missense NM_001385435.1:c.1961C>T NP_001372364.1:p.Thr654Met missense NM_001385436.1:c.1961C>T NP_001372365.1:p.Thr654Met missense NM_001385437.1:c.1961C>T NP_001372366.1:p.Thr654Met missense NM_001385438.1:c.1961C>T NP_001372367.1:p.Thr654Met missense NM_001385439.1:c.1961C>T NP_001372368.1:p.Thr654Met missense NM_001385440.1:c.1961C>T NP_001372369.1:p.Thr654Met missense NM_001385441.1:c.1961C>T NP_001372370.1:p.Thr654Met missense NM_001385442.1:c.1850C>T NP_001372371.1:p.Thr617Met missense NM_001385443.1:c.1850C>T NP_001372372.1:p.Thr617Met missense NM_001385444.1:c.1850C>T NP_001372373.1:p.Thr617Met missense NM_001385445.1:c.1850C>T NP_001372374.1:p.Thr617Met missense NM_001385446.1:c.1736C>T NP_001372375.1:p.Thr579Met missense NM_001385447.1:c.1736C>T NP_001372376.1:p.Thr579Met missense NM_001385448.1:c.2045C>T NP_001372377.1:p.Thr682Met missense NM_173638.5:c.1961C>T NP_775909.2:p.Thr654Met missense NC_000001.11:g.144423065G>A NC_000001.10:g.148594588C>T - Protein change
- T617M, T682M, T654M, T579M
- Other names
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- Canonical SPDI
- NC_000001.11:144423064: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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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- 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. |
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| NBPF15 | - | - |
GRCh38 GRCh37 |
70 | 117 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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May 26, 2024 | RCV004641259.1 |
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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Uncertain significance
(May 26, 2024)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV005145118.1
First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024 |
Comment:
The c.1961C>T (p.T654M) alteration is located in exon 22 (coding exon 15) of the NBPF15 gene. This alteration results from a C to T substitution … (more)
The c.1961C>T (p.T654M) alteration is located in exon 22 (coding exon 15) of the NBPF15 gene. This alteration results from a C to T substitution at nucleotide position 1961, causing the threonine (T) at amino acid position 654 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
|
Comment:
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:
The c.1961C>T (p.T654M) alteration is located in exon 22 (coding exon 15) of the NBPF15 gene. This alteration results from a C to T substitution at nucleotide position 1961, causing the threonine (T) at amino acid position 654 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 this variant ...
HelpRecord last updated Aug 11, 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.