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NM_006096.4(NDRG1):c.789G>A (p.Ser263=) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 11, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002418263.2

Allele description [Variation Report for NM_006096.4(NDRG1):c.789G>A (p.Ser263=)]

NM_006096.4(NDRG1):c.789G>A (p.Ser263=)

Genes:
LOC126860531:CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:134259869-134261068 [Gene]
NDRG1:N-myc downstream regulated 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q24.22
Genomic location:
Preferred name:
NM_006096.4(NDRG1):c.789G>A (p.Ser263=)
HGVS:
  • NC_000008.11:g.133247893C>T
  • NG_007943.1:g.54363G>A
  • NM_001135242.2:c.789G>A
  • NM_001258432.2:c.591G>A
  • NM_001258433.2:c.546G>A
  • NM_001374844.1:c.840G>A
  • NM_001374845.1:c.789G>A
  • NM_001374846.1:c.789G>A
  • NM_001374847.1:c.591G>A
  • NM_006096.4:c.789G>AMANE SELECT
  • NP_001128714.1:p.Ser263=
  • NP_001245361.1:p.Ser197=
  • NP_001245362.1:p.Ser182=
  • NP_001361773.1:p.Ser280=
  • NP_001361774.1:p.Ser263=
  • NP_001361775.1:p.Ser263=
  • NP_001361776.1:p.Ser197=
  • NP_006087.2:p.Ser263=
  • NP_006087.2:p.Ser263=
  • LRG_258t1:c.789G>A
  • LRG_258:g.54363G>A
  • LRG_258p1:p.Ser263=
  • NC_000008.10:g.134260136C>T
  • NM_006096.3:c.789G>A
Links:
dbSNP: rs61755062
NCBI 1000 Genomes Browser:
rs61755062
Molecular consequence:
  • NM_001135242.2:c.789G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001258432.2:c.591G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001258433.2:c.546G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374844.1:c.840G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374845.1:c.789G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374846.1:c.789G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374847.1:c.591G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_006096.4:c.789G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002676897Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jul 11, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002676897.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: May 19, 2024