rs1485768

chr4-176719269-G-A

Variant summary

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

The NM_005429.5(VEGFC):c.553-7619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,124 control chromosomes in the GnomAD database, including 44,323 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 0.72 (44323 hom., cov: 32)
• Consequence: VEGFC NM_005429.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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]

ACMG classification

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 = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEGFC	NM_005429.5	c.553-7619C>T		intron_variant		ENST00000618562.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEGFC	ENST00000618562.2	c.553-7619C>T		intron_variant		1	NM_005429.5	P1
VEGFC	ENST00000507638.1	n.252-7619C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109762 AN: 152006 Hom.: 44323 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.773

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.722 AC: 109783 AN: 152124 Hom.: 44323 Cov.: 32 AF XY: 0.729 AC XY: 54220 AN XY: 74388

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.776

Alfa AF: 0.794 Hom.: 18257

Bravo AF: 0.692

Asia WGS AF: 0.861 AC: 2993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.57
Dann	Benign	0.74

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: rs1485768; hg19: chr4-177640423;