VCV001028135.8 - ClinVar

NM_019023.5(PRMT7):c.499G>A (p.Val167Met)

Germline

Classification

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.

(5)

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.

Conflicting classifications of pathogenicity
Uncertain significance(4); Likely benign(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_019023.5(PRMT7):c.499G>A (p.Val167Met)

Variation ID: 1028135 Accession: VCV001028135.8

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 16q22.1 16: 68337566 (GRCh38) [ NCBI UCSC ] 16: 68371469 (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	Mar 22, 2021	Oct 8, 2024	Sep 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_019023.5:c.499G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061896.1:p.Val167Met	missense
NM_001184824.4:c.349G>A	NP_001171753.1:p.Val117Met	missense
NM_001290018.2:c.499G>A	NP_001276947.1:p.Val167Met	missense
NM_001351143.3:c.499G>A	NP_001338072.1:p.Val167Met	missense
NM_001351144.3:c.499G>A	NP_001338073.1:p.Val167Met	missense
NM_001378018.1:c.499G>A	NP_001364947.1:p.Val167Met	missense
NM_001378020.1:c.292G>A	NP_001364949.1:p.Val98Met	missense
NM_001378021.1:c.262G>A	NP_001364950.1:p.Val88Met	missense
NM_001378022.1:c.262G>A	NP_001364951.1:p.Val88Met	missense
NM_001378023.1:c.262G>A	NP_001364952.1:p.Val88Met	missense
NR_147056.3:n.663G>A		non-coding transcript variant
NR_147057.3:n.798G>A		non-coding transcript variant
NR_147058.3:n.798G>A		non-coding transcript variant
NR_165365.1:n.798G>A		non-coding transcript variant
NR_165366.1:n.663G>A		non-coding transcript variant
NR_165367.1:n.663G>A		non-coding transcript variant
NR_165368.1:n.761G>A		non-coding transcript variant
NR_165369.1:n.626G>A		non-coding transcript variant
NR_165370.1:n.626G>A		non-coding transcript variant
NR_165371.1:n.689G>A		non-coding transcript variant
NR_165372.1:n.798G>A		non-coding transcript variant
NR_165373.1:n.761G>A		non-coding transcript variant
NC_000016.10:g.68337566G>A
NC_000016.9:g.68371469G>A
NG_054896.1:g.31593G>A

... more HGVS ... less HGVS

Protein change

V117M, V88M, V167M, V98M

Other names

Canonical SPDI

NC_000016.10:68337565:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

0.00020 (A)

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.00007

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008

Trans-Omics for Precision Medicine (TOPMed) 0.00008

Exome Aggregation Consortium (ExAC) 0.00011

The Genome Aggregation Database (gnomAD), exomes 0.00011

1000 Genomes Project 30x 0.00016

1000 Genomes Project 0.00020

Links

dbSNP: rs138763605 VarSome

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
Gene	OMIM	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.
PRMT7		-	-	GRCh38 GRCh37	236	272

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.
Short stature-brachydactyly-obesity-global developmental delay syndrome	Conflicting interpretations of pathogenicity (2)	criteria provided, conflicting classifications	Sep 20, 2024	RCV001329104.4
not provided	Uncertain significance (3)	criteria provided, multiple submitters, no conflicts	Feb 9, 2023	RCV001796446.5

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.
Uncertain significance (Aug 01, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Short stature-brachydactyly-obesity-global developmental delay syndrome Affected status: yes Allele origin: unknown	Baylor Genetics Accession: SCV001520432.1 First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021	Comment: This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Uncertain significance (Feb 09, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV002032833.2 First in ClinVar: Dec 18, 2021 Last updated: Feb 18, 2023	Comment: Reported in an individual with leukemia, but additional clinical or segregation information was not provided and this individual was also reported to have multiple variants … (more) Reported in an individual with leukemia, but additional clinical or segregation information was not provided and this individual was also reported to have multiple variants in other genes (Kiel et al., 2015); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25569235, 26415585) (less)
Uncertain significance (Nov 03, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: not provided Allele origin: germline	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden Accession: SCV002011541.3 First in ClinVar: Nov 06, 2021 Last updated: Jul 16, 2023
Uncertain significance (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005193454.1 First in ClinVar: Aug 18, 2024 Last updated: Aug 18, 2024
Likely benign (Sep 20, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Short stature-brachydactyly-obesity-global developmental delay syndrome Affected status: no Allele origin: germline	3billion Accession: SCV005328717.1 First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024	Comment: The homozygous variant was found in patients diagnosed with another variant in a different gene, with no symptoms related to the gene containing the homozygous … (more) The homozygous variant was found in patients diagnosed with another variant in a different gene, with no symptoms related to the gene containing the homozygous variant. (less)

Comment:

Reported in an individual with leukemia, but additional clinical or segregation information was not provided and this individual was also reported to have multiple variants in other genes (Kiel et al., 2015); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25569235, 26415585)

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:

Citations for germline classification of this variant

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 rs138763605 ...

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 Oct 08, 2024

ClinVar Genomic variation as it relates to human health

NM_019023.5(PRMT7):c.499G>A (p.Val167Met)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs138763605 ...