rs3025020

chr6-43781373-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003376.6(VEGFA):c.1034+570C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 247,446 control chromosomes in the GnomAD database, including 9,557 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 0.24 (5105 hom., cov: 34)
  • Exomes 𝑓: 0.29 (4452 hom.)
• Consequence: VEGFA NM_003376.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

VEGFA (HGNC:12680): (vascular endothelial growth factor A) This gene is a member of the PDGF/VEGF growth factor family. It encodes a heparin-binding protein, which exists as a disulfide-linked homodimer. This growth factor induces proliferation and migration of vascular endothelial cells, and is essential for both physiological and pathological angiogenesis. Disruption of this gene in mice resulted in abnormal embryonic blood vessel formation. This gene is upregulated in many known tumors and its expression is correlated with tumor stage and progression. Elevated levels of this protein are found in patients with POEMS syndrome, also known as Crow-Fukase syndrome. Allelic variants of this gene have been associated with microvascular complications of diabetes 1 (MVCD1) and atherosclerosis. Alternatively spliced transcript variants encoding different isoforms have been described. There is also evidence for alternative translation initiation from upstream non-AUG (CUG) codons resulting in additional isoforms. A recent study showed that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is antiangiogenic. Expression of some isoforms derived from the AUG start codon is regulated by a small upstream open reading frame, which is located within an internal ribosome entry site. The levels of VEGF are increased during infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus promoting inflammation by facilitating recruitment of inflammatory cells, and by increasing the level of angiopoietin II (Ang II), one of two products of the SARS-CoV-2 binding target, angiotensin-converting enzyme 2 (ACE2). In turn, Ang II facilitates the elevation of VEGF, thus forming a vicious cycle in the release of inflammatory cytokines. [provided by RefSeq, Jun 2020]

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEGFA	NM_003376.6	c.1034+570C>T		intron_variant		ENST00000672860.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEGFA	ENST00000672860.3	c.1034+570C>T		intron_variant			NM_003376.6

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36417 AN: 152112 Hom.: 5107 Cov.: 34

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.290 AC: 27652 AN: 95216 Hom.: 4452 Cov.: 0 AF XY: 0.299 AC XY: 15039 AN XY: 50300

Gnomad4 AFR exome AF: 0.0782

Gnomad4 AMR exome AF: 0.279

Gnomad4 ASJ exome AF: 0.288

Gnomad4 EAS exome AF: 0.340

Gnomad4 SAS exome AF: 0.366

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.278

GnomAD4 genome AF: 0.239 AC: 36431 AN: 152230 Hom.: 5105 Cov.: 34 AF XY: 0.242 AC XY: 17997 AN XY: 74428

Gnomad4 AFR AF: 0.0891

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.238

Alfa AF: 0.270 Hom.: 1340

Bravo AF: 0.231

Asia WGS AF: 0.277 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.3
Dann	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3025020; hg19: chr6-43749110;