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NM_000090.4(COL3A1):c.3299G>A (p.Arg1100His) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Sep 3, 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:
RCV001194122.1

Allele description [Variation Report for NM_000090.4(COL3A1):c.3299G>A (p.Arg1100His)]

NM_000090.4(COL3A1):c.3299G>A (p.Arg1100His)

Gene:
COL3A1:collagen type III alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q32.2
Genomic location:
Preferred name:
NM_000090.4(COL3A1):c.3299G>A (p.Arg1100His)
HGVS:
  • NC_000002.12:g.189007543G>A
  • NG_007404.1:g.38171G>A
  • NM_000090.4:c.3299G>AMANE SELECT
  • NP_000081.2:p.Arg1100His
  • LRG_3t1:c.3299G>A
  • LRG_3:g.38171G>A
  • NC_000002.11:g.189872269G>A
  • NM_000090.3:c.3299G>A
Protein change:
R1100H
Links:
dbSNP: rs370069953
NCBI 1000 Genomes Browser:
rs370069953
Molecular consequence:
  • NM_000090.4:c.3299G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001363411Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Sep 3, 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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363411.1

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

Description

Variant summary: COL3A1 c.3299G>A (p.Arg1100His) results in a non-conservative amino acid change located in the Collagen triple helix repeat (IPR008160) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.3e-05 in 282104 control chromosomes (gnomAD). The observed variant frequency is approximately 34 fold of the estimated maximal expected allele frequency for a pathogenic variant in COL3A1 causing Aortopathy phenotype (1.3e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.3299G>A in individuals affected with Aortopathy and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely benign.

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

Last Updated: Jun 2, 2024