NM_000094.4(COL7A1):c.4859G>A (p.Arg1620Gln) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001355646.1

Allele description [Variation Report for NM_000094.4(COL7A1):c.4859G>A (p.Arg1620Gln)]

NM_000094.4(COL7A1):c.4859G>A (p.Arg1620Gln)

Gene:
COL7A1:collagen type VII alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_000094.4(COL7A1):c.4859G>A (p.Arg1620Gln)
HGVS:
  • NC_000003.12:g.48581300C>T
  • NG_007065.1:g.18953G>A
  • NM_000094.4:c.4859G>AMANE SELECT
  • NP_000085.1:p.Arg1620Gln
  • LRG_286:g.18953G>A
  • NC_000003.11:g.48618733C>T
Protein change:
R1620Q
Molecular consequence:
  • NM_000094.4:c.4859G>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
SCV001550589Department 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 providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550589.1

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

Description

The COL7A1 p.Arg1620Gln variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs373682717) and Cosmic. The variant was identified in control databases in 23 of 280948 chromosomes at a frequency of 0.000082 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 13 of 24576 chromosomes (freq: 0.000529), European (Finnish) in 8 of 25060 chromosomes (freq: 0.000319), Other in 1 of 7170 chromosomes (freq: 0.00014) and European (non-Finnish) in 1 of 127980 chromosomes (freq: 0.000008), it was not observed in the Latino, Ashkenazi Jewish, East Asian, and South Asian populations. The p.Arg1620 residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; 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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