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NM_005522.5(HOXA1):c.786C>T (p.Ile262=) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 16, 2020
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:
RCV002412260.2

Allele description [Variation Report for NM_005522.5(HOXA1):c.786C>T (p.Ile262=)]

NM_005522.5(HOXA1):c.786C>T (p.Ile262=)

Gene:
HOXA1:homeobox A1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p15.2
Genomic location:
Preferred name:
NM_005522.5(HOXA1):c.786C>T (p.Ile262=)
HGVS:
  • NC_000007.14:g.27094662G>A
  • NG_011813.1:g.6345C>T
  • NG_011813.2:g.6338C>T
  • NG_033087.1:g.3569G>A
  • NG_033087.2:g.3570G>A
  • NG_115642.1:g.676G>A
  • NG_115643.1:g.175G>A
  • NM_005522.5:c.786C>TMANE SELECT
  • NM_153620.3:c.*169C>T
  • NP_005513.2:p.Ile262=
  • NC_000007.13:g.27134281G>A
  • NM_005522.4:c.786C>T
Molecular consequence:
  • NM_153620.3:c.*169C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_005522.5:c.786C>T - 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
SCV002676811Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Mar 16, 2020) 		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, SCV002676811.2

#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 1, 2024