chr5-77035645-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018046.5(AGGF1):c.418A>G(p.Lys140Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018046.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGGF1 | NM_018046.5 | c.418A>G | p.Lys140Glu | missense_variant | 3/14 | ENST00000312916.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGGF1 | ENST00000312916.12 | c.418A>G | p.Lys140Glu | missense_variant | 3/14 | 1 | NM_018046.5 | P1 | |
AGGF1 | ENST00000506806.1 | c.418A>G | p.Lys140Glu | missense_variant | 3/3 | 1 | |||
AGGF1 | ENST00000502408.1 | c.*144A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/5 | 1 | ||||
AGGF1 | ENST00000503538.5 | n.435A>G | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251284Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135826
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461320Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726998
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at