X-15381161-A-G

Position:

• chrX-15381161-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004469.5(VEGFD):​c.90+2696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (21021 hom., 23708 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: VEGFD NM_004469.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

Genes affected

VEGFD (HGNC:3708): (vascular endothelial growth factor D) The protein encoded by this gene is a member of the platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF) family and is active in angiogenesis, lymphangiogenesis, and endothelial cell growth. This secreted protein undergoes a complex proteolytic maturation, generating multiple processed forms which bind and activate VEGFR-2 and VEGFR-3 receptors. This protein is structurally and functionally similar to vascular endothelial growth factor C. Read-through transcription has been observed between this locus and the upstream PIR (GeneID 8544) locus. [provided by RefSeq, Feb 2011]

PIR-FIGF (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VEGFD	NM_004469.5	c.90+2696T>C		intron_variant		ENST00000297904.4	NP_004460.1
PIR-FIGF	NR_037859.2	n.1065+9024T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VEGFD	ENST00000297904.4	c.90+2696T>C		intron_variant		1	NM_004469.5	ENSP00000297904.3

Frequencies

GnomAD3 genomes AF: 0.722 AC: 79717 AN: 110340 Hom.: 21019 Cov.: 23 AF XY: 0.727 AC XY: 23649 AN XY: 32550

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.712

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.723 AC: 79776 AN: 110394 Hom.: 21021 Cov.: 23 AF XY: 0.727 AC XY: 23708 AN XY: 32614

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.716

Alfa AF: 0.641 Hom.: 41748

Bravo AF: 0.737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
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: rs4830939; hg19: chrX-15399283;