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NM_002528.7(NTHL1):c.313C>T (p.Leu105=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 21, 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:
RCV001020142.3

Allele description [Variation Report for NM_002528.7(NTHL1):c.313C>T (p.Leu105=)]

NM_002528.7(NTHL1):c.313C>T (p.Leu105=)

Gene:
NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_002528.7(NTHL1):c.313C>T (p.Leu105=)
HGVS:
  • NC_000016.10:g.2046169G>A
  • NG_005895.1:g.1864G>A
  • NG_008412.1:g.6698C>T
  • NM_001318193.2:c.313C>T
  • NM_001318194.2:c.24+111C>T
  • NM_002528.7:c.313C>TMANE SELECT
  • NP_001305122.2:p.Leu105=
  • NP_002519.2:p.Leu105=
  • LRG_1366t1:c.313C>T
  • LRG_1366:g.6698C>T
  • LRG_1366p1:p.Leu105=
  • LRG_487:g.1864G>A
  • NC_000016.9:g.2096170G>A
  • NC_000016.9:g.2096170G>A
  • NM_002528.5:c.337C>T
Links:
dbSNP: rs1386204098
NCBI 1000 Genomes Browser:
rs1386204098
Molecular consequence:
  • NM_001318194.2:c.24+111C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318193.2:c.313C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_002528.7:c.313C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001181583Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Aug 21, 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, SCV001181583.4

#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: Sep 29, 2024