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NM_006623.4(PHGDH):c.792+6T>G AND not provided

Germline classification:
Benign/Likely benign (4 submissions)
Last evaluated:
Jul 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000518662.24

Allele description [Variation Report for NM_006623.4(PHGDH):c.792+6T>G]

NM_006623.4(PHGDH):c.792+6T>G

Gene:
PHGDH:phosphoglycerate dehydrogenase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p12
Genomic location:
Preferred name:
NM_006623.4(PHGDH):c.792+6T>G
HGVS:
  • NC_000001.11:g.119735449T>G
  • NG_009188.1:g.28654T>G
  • NM_006623.4:c.792+6T>GMANE SELECT
  • NC_000001.10:g.120278072T>G
  • NM_006623.3:c.792+6T>G
Links:
dbSNP: rs146953046
NCBI 1000 Genomes Browser:
rs146953046
Molecular consequence:
  • NM_006623.4:c.792+6T>G - intron variant - [Sequence Ontology: SO:0001627]
Observations:
30

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000614448Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)
Benign
(Feb 21, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001850812GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Mar 30, 2021)
germlineclinical testing

Citation Link,

SCV002496908CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Benign
(Jul 1, 2024)
germlineclinical testing

Citation Link,

SCV005261554Breakthrough Genomics, Breakthrough Genomics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benigngermlinenot provided

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes30not providednot providednot providednot providedclinical testing, not provided
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Athena Diagnostics, SCV000614448.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001850812.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is associated with the following publications: (PMID: 33087887)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV002496908.18

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided30not providednot providedclinical testingnot provided

Description

PHGDH: BP4, BS1, BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided30not providednot providednot provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005261554.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024