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NM_057175.5(NAA15):c.55-2A>C AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 12, 2019
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001255020.2

Allele description [Variation Report for NM_057175.5(NAA15):c.55-2A>C]

NM_057175.5(NAA15):c.55-2A>C

Gene:
NAA15:N-alpha-acetyltransferase 15, NatA auxiliary subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q31.1
Genomic location:
Preferred name:
NM_057175.5(NAA15):c.55-2A>C
HGVS:
  • NC_000004.12:g.139334172A>C
  • NG_053037.1:g.37706A>C
  • NM_001410842.1:c.55-2A>C
  • NM_057175.5:c.55-2A>CMANE SELECT
  • NC_000004.11:g.140255326A>C
  • NM_057175.3:c.55-2A>C
  • NM_057175.4:c.55-2A>C
Links:
Molecular consequence:
  • NM_001410842.1:c.55-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_057175.5:c.55-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

Condition(s)

Name:
Autism (AUTS)
Synonyms:
Autistic disorder; Autistic disorder of childhood onset
Identifiers:
MONDO: MONDO:0005260; MeSH: D001321; MedGen: C0004352; OMIM: 209850; Human Phenotype Ontology: HP:0000717
Name:
Focal-onset seizure
Synonyms:
Focal seizures
Identifiers:
MedGen: C0751495; Human Phenotype Ontology: HP:0007359
Name:
Intellectual disability
Synonyms:
Intellectual functioning disability; intellectual disabilities; Intellectual developmental disorder
Identifiers:
MONDO: MONDO:0001071; MeSH: D008607; MedGen: C3714756; Human Phenotype Ontology: HP:0001249

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001431110New York Genome Center
no assertion criteria provided
Likely pathogenic
(Nov 12, 2019) 		de novoclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV001431110.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

This variant substitutes a completely conserved adenine for cytosine at the canonical splice acceptor site within intron 1/19. This variant is absent from gnomAD and ExAC suggesting it is not a common benign variant in the populations represented in these databases. To our current knowledge has not been reported in affected individuals in the literature, however other nonsense, frameshift, and canonical splice variants have been reported. This variant was identified de novo in an individual referred for clinical WGS testing in our laboratory.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyes1not providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024