chr5-77046622-T-C
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_018046.5(AGGF1):c.1146T>C(p.Tyr382=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00413 in 1,614,038 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0042 ( 27 hom. )
Consequence
AGGF1
NM_018046.5 synonymous
NM_018046.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.377
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 5-77046622-T-C is Benign according to our data. Variant chr5-77046622-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 777169.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.377 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGGF1 | NM_018046.5 | c.1146T>C | p.Tyr382= | synonymous_variant | 6/14 | ENST00000312916.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGGF1 | ENST00000312916.12 | c.1146T>C | p.Tyr382= | synonymous_variant | 6/14 | 1 | NM_018046.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00367 AC: 559AN: 152194Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00432 AC: 1086AN: 251276Hom.: 12 AF XY: 0.00421 AC XY: 572AN XY: 135824
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GnomAD4 exome AF: 0.00418 AC: 6110AN: 1461726Hom.: 27 Cov.: 32 AF XY: 0.00413 AC XY: 3000AN XY: 727152
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GnomAD4 genome ? AF: 0.00367 AC: 559AN: 152312Hom.: 1 Cov.: 33 AF XY: 0.00379 AC XY: 282AN XY: 74476
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | AGGF1: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at