5-77039662-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018046.5(AGGF1):c.813T>A(p.Asp271Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,612,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018046.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGGF1 | NM_018046.5 | c.813T>A | p.Asp271Glu | missense_variant | 5/14 | ENST00000312916.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGGF1 | ENST00000312916.12 | c.813T>A | p.Asp271Glu | missense_variant | 5/14 | 1 | NM_018046.5 | P1 | |
AGGF1 | ENST00000502408.1 | c.*539T>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249206Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134838
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1459998Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726146
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.813T>A (p.D271E) alteration is located in exon 5 (coding exon 5) of the AGGF1 gene. This alteration results from a T to A substitution at nucleotide position 813, causing the aspartic acid (D) at amino acid position 271 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at