rs7704267

Positions:

• chr5-77058177-C-G
• chr5-77058177-C-T

Variant summary

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

The NM_018046.5(AGGF1):​c.1717-1439C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,932 control chromosomes in the GnomAD database, including 25,634 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 0.58 (25634 hom., cov: 32)
• Consequence: AGGF1 NM_018046.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

Genes affected

AGGF1 (HGNC:24684): (angiogenic factor with G-patch and FHA domains 1) This gene encodes an angiogenic factor that promotes proliferation of endothelial cells. Mutations in this gene are associated with a susceptibility to Klippel-Trenaunay syndrome. Pseudogenes of this gene are found on chromosomes 3, 4, 10 and 16.[provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGGF1	NM_018046.5	c.1717-1439C>G		intron_variant		ENST00000312916.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGGF1	ENST00000312916.12	c.1717-1439C>G		intron_variant		1	NM_018046.5	P1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87489 AN: 151814 Hom.: 25627 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.576 AC: 87532 AN: 151932 Hom.: 25634 Cov.: 32 AF XY: 0.579 AC XY: 43007 AN XY: 74250

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.607

Alfa AF: 0.461 Hom.: 1302

Bravo AF: 0.572

Asia WGS AF: 0.479 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7704267; hg19: chr5-76354002;