NM_001080414.4(CCDC88C):c.4375G>A (p.Asp1459Asn) AND not provided

Clinical significance:Likely benign (Last evaluated: Oct 23, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000939719.2

Allele description [Variation Report for NM_001080414.4(CCDC88C):c.4375G>A (p.Asp1459Asn)]

NM_001080414.4(CCDC88C):c.4375G>A (p.Asp1459Asn)

Gene:
CCDC88C:coiled-coil domain containing 88C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q32.11
Genomic location:
Preferred name:
NM_001080414.4(CCDC88C):c.4375G>A (p.Asp1459Asn)
HGVS:
  • NC_000014.9:g.91289171C>T
  • NG_033118.1:g.133674G>A
  • NG_033118.2:g.133674G>A
  • NM_001080414.4:c.4375G>AMANE SELECT
  • NP_001073883.2:p.Asp1459Asn
  • NC_000014.8:g.91755515C>T
  • NM_001080414.3:c.4375G>A
Protein change:
D1459N
Links:
dbSNP: rs78570354
NCBI 1000 Genomes Browser:
rs78570354
Molecular consequence:
  • NM_001080414.4:c.4375G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001085569Invitaecriteria provided, single submitter
Likely benign
(Oct 23, 2018)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001550376Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001085569.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550376.1

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

Description

The CCDC88C p.Asp1459Asn variant was not identified in the literature nor was it identified in ClinVar, Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs78570354) and in control databases in 99 of 278450 chromosomes at a frequency of 0.000356 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 95 of 19516 chromosomes (freq: 0.004868), African in 3 of 24164 chromosomes (freq: 0.000124) and European (non-Finnish) in 1 of 126370 chromosomes (freq: 0.000008), but not in the Latino, Ashkenazi Jewish, European (Finnish), Other, and South Asian populations. The p.Asp1459 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Apr 12, 2021

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