4-176699956-T-G

Variant summary

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

The NM_005429.5(VEGFC):c.704+11543A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,144 control chromosomes in the GnomAD database, including 44,282 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 0.76 (44282 hom., cov: 33)
• Consequence: VEGFC NM_005429.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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]

HAFML (HGNC:56694): (HuR (ELAVL1) associated fibroblast migratory lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEGFC	NM_005429.5	c.704+11543A>C		intron_variant		ENST00000618562.2
HAFML	NR_183975.1	n.183-5947T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEGFC	ENST00000618562.2	c.704+11543A>C		intron_variant		1	NM_005429.5	P1
HAFML	ENST00000509194.1	n.90-5947T>G		intron_variant, non_coding_transcript_variant		3
HAFML	ENST00000504017.5	n.141-5947T>G		intron_variant, non_coding_transcript_variant		2
VEGFC	ENST00000507638.1	n.404-10301A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115516 AN: 152026 Hom.: 44233 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.760 AC: 115622 AN: 152144 Hom.: 44282 Cov.: 33 AF XY: 0.756 AC XY: 56191 AN XY: 74360

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.765

Alfa AF: 0.732 Hom.: 52612

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.37
Dann	Benign	0.51

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: rs3775195; hg19: chr4-177621110;