rs151317075
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002253.4(KDR):c.1055C>T(p.Ala352Val) variant causes a missense change. The variant allele was found at a frequency of 0.000285 in 1,613,304 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 2 hom. )
Consequence
KDR
NM_002253.4 missense
NM_002253.4 missense
Scores
1
13
Clinical Significance
Conservation
PhyloP100: 4.90
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=0.009578437).
BP6
?
Variant 4-55110690-G-A is Benign according to our data. Variant chr4-55110690-G-A is described in ClinVar as [Benign]. Clinvar id is 134617.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd4 at 208 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDR | NM_002253.4 | c.1055C>T | p.Ala352Val | missense_variant | 8/30 | ENST00000263923.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDR | ENST00000263923.5 | c.1055C>T | p.Ala352Val | missense_variant | 8/30 | 1 | NM_002253.4 | P1 | |
KDR | ENST00000512566.1 | n.1055C>T | non_coding_transcript_exon_variant | 8/13 | 1 | ||||
KDR | ENST00000647068.1 | n.1068C>T | non_coding_transcript_exon_variant | 8/30 |
Frequencies
GnomAD3 genomes ? AF: 0.00138 AC: 209AN: 151416Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000386 AC: 97AN: 251298Hom.: 1 AF XY: 0.000331 AC XY: 45AN XY: 135856
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GnomAD4 exome AF: 0.000172 AC: 251AN: 1461772Hom.: 2 Cov.: 33 AF XY: 0.000150 AC XY: 109AN XY: 727200
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GnomAD4 genome ? AF: 0.00137 AC: 208AN: 151532Hom.: 0 Cov.: 32 AF XY: 0.00135 AC XY: 100AN XY: 73984
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
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
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N
PrimateAI
Uncertain
T
Polyphen
B;B
Vest4
0.35
MVP
0.10
MPC
0.16
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