rs7704267

Variant names:

• chr5-77058177-C-G
• rs7704267
• NM_018046.5:c.1717-1439C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000285000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AGGF1	NM_018046.5	c.1717-1439C>G		intron_variant	Intron 11 of 13	ENST00000312916.12	NP_060516.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGGF1	ENST00000312916.12	c.1717-1439C>G		intron_variant	Intron 11 of 13	1	NM_018046.5	ENSP00000316109.7
ENSG00000285000	ENST00000646704.1	n.1582-1439C>G		intron_variant	Intron 11 of 15			ENSP00000495089.1

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

African (AFR) AF: 0.488 AC: 20214 AN: 41402

American (AMR) AF: 0.611 AC: 9340 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2031 AN: 3460

East Asian (EAS) AF: 0.587 AC: 3029 AN: 5158

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4822

European-Finnish (FIN) AF: 0.697 AC: 7351 AN: 10542

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41544 AN: 67962

Other (OTH) AF: 0.607 AC: 1278 AN: 2104

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
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7704267; hg19: chr5-76354002;