chr2-227534999-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004504.5(AGFG1):c.1179G>A(p.Ala393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,612,882 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00043 ( 1 hom. )
Consequence
AGFG1
NM_004504.5 synonymous
NM_004504.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
Genes affected
AGFG1 (HGNC:5175): (ArfGAP with FG repeats 1) The protein encoded by this gene is related to nucleoporins, a class of proteins that mediate nucleocytoplasmic transport. The encoded protein binds the activation domain of the human immunodeficiency virus Rev protein when Rev is assembled onto its RNA target, and is required for the nuclear export of Rev-directed RNAs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 2-227534999-G-A is Benign according to our data. Variant chr2-227534999-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651961.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.54 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGFG1 | NM_004504.5 | c.1179G>A | p.Ala393= | synonymous_variant | 8/13 | ENST00000310078.13 | |
AGFG1 | NM_001135187.2 | c.1251G>A | p.Ala417= | synonymous_variant | 9/14 | ||
AGFG1 | NM_001135188.2 | c.1179G>A | p.Ala393= | synonymous_variant | 8/13 | ||
AGFG1 | NM_001135189.2 | c.1059G>A | p.Ala353= | synonymous_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGFG1 | ENST00000310078.13 | c.1179G>A | p.Ala393= | synonymous_variant | 8/13 | 1 | NM_004504.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152058Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000315 AC: 79AN: 250484Hom.: 0 AF XY: 0.000325 AC XY: 44AN XY: 135410
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GnomAD4 exome AF: 0.000425 AC: 621AN: 1460824Hom.: 1 Cov.: 32 AF XY: 0.000400 AC XY: 291AN XY: 726724
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GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74258
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | AGFG1: BP4, BP7 - |
Computational scores
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Name
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Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at