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NM_000213.5(ITGB4):c.1345G>A (p.Gly449Ser) AND not provided

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jan 28, 2024
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:
RCV001355124.6

Allele description [Variation Report for NM_000213.5(ITGB4):c.1345G>A (p.Gly449Ser)]

NM_000213.5(ITGB4):c.1345G>A (p.Gly449Ser)

Gene:
ITGB4:integrin subunit beta 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.1
Genomic location:
Preferred name:
NM_000213.5(ITGB4):c.1345G>A (p.Gly449Ser)
HGVS:
  • NC_000017.11:g.75731941G>A
  • NG_007372.1:g.15507G>A
  • NM_000213.5:c.1345G>AMANE SELECT
  • NM_001005619.1:c.1345G>A
  • NM_001005731.3:c.1345G>A
  • NM_001321123.2:c.1345G>A
  • NP_000204.3:p.Gly449Ser
  • NP_001005619.1:p.Gly449Ser
  • NP_001005731.1:p.Gly449Ser
  • NP_001308052.1:p.Gly449Ser
  • NC_000017.10:g.73728022G>A
  • NC_000017.10:g.73728022G>A
  • NM_001005731.1:c.1345G>A
  • NM_001005731.2:c.1345G>A
Protein change:
G449S
Links:
dbSNP: rs147963396
NCBI 1000 Genomes Browser:
rs147963396
Molecular consequence:
  • NM_000213.5:c.1345G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005619.1:c.1345G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005731.3:c.1345G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321123.2:c.1345G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001549913Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

SCV002203702Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 28, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001549913.1

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

Description

The ITGB4 p.Gly449Ser 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: rs147963396) and in control databases in 187 of 282486 chromosomes at a frequency of 0.000662 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 164 of 128888 chromosomes (freq: 0.001272), Other in 4 of 7218 chromosomes (freq: 0.000554), Latino in 11 of 35422 chromosomes (freq: 0.000311), European (Finnish) in 7 of 25110 chromosomes (freq: 0.000279) and South Asian in 1 of 30616 chromosomes (freq: 0.000033); it was not observed in the African, Ashkenazi Jewish or East Asian populations. 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. The p.Gly449 residue is not conserved in mammals or distantly related organisms 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. 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

From Invitae, SCV002203702.3

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

Last Updated: Feb 20, 2024