rs34038364
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002253.4(KDR):c.2066C>T(p.Thr689Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,613,602 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 12 hom. )
Consequence
KDR
NM_002253.4 missense
NM_002253.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.0930
Genes affected
KDR (HGNC:6307): (kinase insert domain receptor) Vascular endothelial growth factor (VEGF) is a major growth factor for endothelial cells. This gene encodes one of the two receptors of the VEGF. This receptor, known as kinase insert domain receptor, is a type III receptor tyrosine kinase. It functions as the main mediator of VEGF-induced endothelial proliferation, survival, migration, tubular morphogenesis and sprouting. The signalling and trafficking of this receptor are regulated by multiple factors, including Rab GTPase, P2Y purine nucleotide receptor, integrin alphaVbeta3, T-cell protein tyrosine phosphatase, etc.. Mutations of this gene are implicated in infantile capillary hemangiomas. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0052033663).
BP6
Variant 4-55102430-G-A is Benign according to our data. Variant chr4-55102430-G-A is described in ClinVar as [Benign]. Clinvar id is 134606.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-55102430-G-A is described in Lovd as [Likely_benign].
BS2
High AC in GnomAd4 at 443 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDR | NM_002253.4 | c.2066C>T | p.Thr689Met | missense_variant | 14/30 | ENST00000263923.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDR | ENST00000263923.5 | c.2066C>T | p.Thr689Met | missense_variant | 14/30 | 1 | NM_002253.4 | P1 | |
KDR | ENST00000647068.1 | n.2079C>T | non_coding_transcript_exon_variant | 14/30 |
Frequencies
GnomAD3 genomes AF: 0.00291 AC: 443AN: 152138Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00319 AC: 800AN: 251160Hom.: 7 AF XY: 0.00297 AC XY: 403AN XY: 135738
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GnomAD4 exome AF: 0.00336 AC: 4916AN: 1461346Hom.: 12 Cov.: 32 AF XY: 0.00322 AC XY: 2344AN XY: 726994
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GnomAD4 genome AF: 0.00291 AC: 443AN: 152256Hom.: 1 Cov.: 32 AF XY: 0.00353 AC XY: 263AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:2Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The KDR p.Thr689Met variant was not identified in the literature but was identified in dbSNP (ID: rs34038364), ClinVar (classified as uncertain significance by Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville) and LOVD 3.0 (classified as likely benign). The variant was identified in control databases in 916 of 282566 chromosomes (7 homozygous) at a frequency of 0.003242 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (Finnish) in 370 of 25118 chromosomes (freq: 0.01473), Other in 40 of 7210 chromosomes (freq: 0.005548), European (non-Finnish) in 392 of 128968 chromosomes (freq: 0.00304), Latino in 92 of 35386 chromosomes (freq: 0.0026), African in 21 of 24964 chromosomes (freq: 0.000841) and Ashkenazi Jewish in 1 of 10360 chromosomes (freq: 0.000097), but was not observed in the East Asian or South Asian populations. The p.Thr689 residue is not conserved in mammals and four out of five 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign. - |
Hirschsprung disease, susceptibility to, 1 Uncertain:1
Uncertain significance, no assertion criteria provided | research | Department of Genetics, Reproduction and Fetal Medicine., Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville. | Apr 01, 2015 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
.;N
REVEL
Benign
Sift
Benign
.;T
Sift4G
Benign
.;T
Polyphen
B;B
Vest4
0.22
MVP
0.082
MPC
0.17
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at