4-176685497-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005429.5(VEGFC):c.1146-1457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 152,232 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.023 ( 64 hom., cov: 33)
Consequence
VEGFC
NM_005429.5 intron
NM_005429.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0250
Genes affected
VEGFC (HGNC:12682): (vascular endothelial growth factor C) The protein encoded by this gene is a member of the platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF) family. The encoded protein promotes angiogenesis and endothelial cell growth, and can also affect the permeability of blood vessels. The proprotein is further cleaved into a fully processed form that can bind and activate VEGFR-2 and VEGFR-3 receptors. [provided by RefSeq, Apr 2014]
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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=-0.91).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0233 (3551/152232) while in subpopulation NFE AF= 0.0358 (2432/67994). AF 95% confidence interval is 0.0346. There are 64 homozygotes in gnomad4. There are 1692 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3551 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VEGFC | NM_005429.5 | c.1146-1457A>G | intron_variant | ENST00000618562.2 | NP_005420.1 | |||
HAFML | NR_183975.1 | n.182+15788T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VEGFC | ENST00000618562.2 | c.1146-1457A>G | intron_variant | 1 | NM_005429.5 | ENSP00000480043.1 | ||||
ENSG00000248388 | ENST00000504017.5 | n.140+5747T>C | intron_variant | 2 | ||||||
ENSG00000248388 | ENST00000509194.1 | n.89+15788T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0234 AC: 3553AN: 152112Hom.: 64 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0233 AC: 3551AN: 152232Hom.: 64 Cov.: 33 AF XY: 0.0227 AC XY: 1692AN XY: 74442
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ClinVar
Not reported inComputational 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