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NM_003640.5(ELP1):c.888A>G (p.Ala296=) AND not specified

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jul 11, 2019
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:
RCV000439637.2

Allele description [Variation Report for NM_003640.5(ELP1):c.888A>G (p.Ala296=)]

NM_003640.5(ELP1):c.888A>G (p.Ala296=)

Gene:
ELP1:elongator acetyltransferase complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q31.3
Genomic location:
Preferred name:
NM_003640.5(ELP1):c.888A>G (p.Ala296=)
HGVS:
  • NC_000009.12:g.108916274T>C
  • NG_008788.1:g.23055A>G
  • NM_001318360.2:c.546A>G
  • NM_001330749.2:c.-160A>G
  • NM_003640.5:c.888A>GMANE SELECT
  • NP_001305289.1:p.Ala182=
  • NP_003631.2:p.Ala296=
  • LRG_251t1:c.888A>G
  • LRG_251:g.23055A>G
  • NC_000009.11:g.111678554T>C
  • NM_003640.3:c.888A>G
Links:
dbSNP: rs371923882
NCBI 1000 Genomes Browser:
rs371923882
Molecular consequence:
  • NM_001330749.2:c.-160A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001318360.2:c.546A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_003640.5:c.888A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000529186GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Likely benign
(Jul 7, 2016)
germlineclinical testing

Citation Link,

SCV002755125Ambry Genetics
criteria provided, single submitter

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

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000529186.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Ambry Genetics, SCV002755125.2

#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: Nov 24, 2024