rs17085310
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002253.4(KDR):c.1987+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,580,432 control chromosomes in the GnomAD database, including 709 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.014 ( 73 hom., cov: 32)
Exomes 𝑓: 0.011 ( 636 hom. )
Consequence
KDR
NM_002253.4 intron
NM_002253.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.658
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0789 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDR | NM_002253.4 | c.1987+28C>T | intron_variant | ENST00000263923.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDR | ENST00000263923.5 | c.1987+28C>T | intron_variant | 1 | NM_002253.4 | P1 | |||
KDR | ENST00000512566.1 | n.2015C>T | non_coding_transcript_exon_variant | 13/13 | 1 | ||||
KDR | ENST00000647068.1 | n.2000+28C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0136 AC: 2072AN: 152128Hom.: 73 Cov.: 32
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GnomAD3 exomes AF: 0.0303 AC: 7393AN: 244128Hom.: 366 AF XY: 0.0262 AC XY: 3458AN XY: 132090
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GnomAD4 exome AF: 0.0110 AC: 15678AN: 1428186Hom.: 636 Cov.: 28 AF XY: 0.0109 AC XY: 7780AN XY: 712138
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GnomAD4 genome ? AF: 0.0136 AC: 2069AN: 152246Hom.: 73 Cov.: 32 AF XY: 0.0154 AC XY: 1149AN XY: 74418
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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