X-15381161-A-G

Variant names:

• chrX-15381161-A-G
• rs4830939
• NM_004469.5:c.90+2696T>C

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004469.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VEGFD	NM_004469.5	MANE Select	c.90+2696T>C		intron	N/A	NP_004460.1
	PIR-FIGF	NR_037859.2		n.1065+9024T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VEGFD	ENST00000297904.4	TSL:1 MANE Select	c.90+2696T>C		intron	N/A	ENSP00000297904.3
	VEGFD	ENST00000948564.1		c.90+2696T>C		intron	N/A	ENSP00000618623.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 79717 AN: 110340 Hom.: 21019 Cov.: 23

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

African (AFR) AF: 0.916 AC: 27848 AN: 30400

American (AMR) AF: 0.725 AC: 7505 AN: 10350

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1400 AN: 2632

East Asian (EAS) AF: 0.957 AC: 3375 AN: 3525

South Asian (SAS) AF: 0.852 AC: 2190 AN: 2571

European-Finnish (FIN) AF: 0.673 AC: 3834 AN: 5696

Middle Eastern (MID) AF: 0.577 AC: 124 AN: 215

European-Non Finnish (NFE) AF: 0.607 AC: 32064 AN: 52826

Other (OTH) AF: 0.716 AC: 1077 AN: 1504

Alfa AF: 0.652 Hom.: 56313

Bravo AF: 0.737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.74
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4830939; hg19: chrX-15399283;