chr5-77036593-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018046.5(AGGF1):c.554T>C(p.Leu185Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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.554T>C | p.Leu185Ser | missense_variant | 4/14 | ENST00000312916.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGGF1 | ENST00000312916.12 | c.554T>C | p.Leu185Ser | missense_variant | 4/14 | 1 | NM_018046.5 | P1 | |
AGGF1 | ENST00000502408.1 | c.*280T>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 1 | ||||
AGGF1 | ENST00000503538.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251300Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135810
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461824Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727214
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.554T>C (p.L185S) alteration is located in exon 4 (coding exon 4) of the AGGF1 gene. This alteration results from a T to C substitution at nucleotide position 554, causing the leucine (L) at amino acid position 185 to be replaced by a serine (S). 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