chr5-77035624-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PS1_ModerateBP4_StrongBP6_Very_StrongBS1BS2
The NM_018046.5(AGGF1):c.397G>A(p.Glu133Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,613,410 control chromosomes in the GnomAD database, including 196 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_018046.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGGF1 | NM_018046.5 | c.397G>A | p.Glu133Lys | missense_variant | 3/14 | ENST00000312916.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGGF1 | ENST00000312916.12 | c.397G>A | p.Glu133Lys | missense_variant | 3/14 | 1 | NM_018046.5 | P1 | |
AGGF1 | ENST00000506806.1 | c.397G>A | p.Glu133Lys | missense_variant | 3/3 | 1 | |||
AGGF1 | ENST00000502408.1 | c.*123G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/5 | 1 | ||||
AGGF1 | ENST00000503538.5 | n.414G>A | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00998 AC: 1518AN: 152052Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.0102 AC: 2555AN: 251246Hom.: 24 AF XY: 0.0102 AC XY: 1392AN XY: 135810
GnomAD4 exome AF: 0.0142 AC: 20774AN: 1461240Hom.: 182 Cov.: 31 AF XY: 0.0140 AC XY: 10210AN XY: 726942
GnomAD4 genome AF: 0.00997 AC: 1517AN: 152170Hom.: 14 Cov.: 33 AF XY: 0.00913 AC XY: 679AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | AGGF1: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2018 | This variant is associated with the following publications: (PMID: 27884173, 14961121, 16443853) - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 185/13004=1.4% - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at