chr7-135034366-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178563.4(AGBL3):c.775A>C(p.Ile259Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178563.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL3 | NM_178563.4 | c.775A>C | p.Ile259Leu | missense_variant | 7/17 | ENST00000436302.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL3 | ENST00000436302.6 | c.775A>C | p.Ile259Leu | missense_variant | 7/17 | 2 | NM_178563.4 | P2 | |
AGBL3 | ENST00000275763.10 | c.775A>C | p.Ile259Leu | missense_variant, NMD_transcript_variant | 7/17 | 1 | |||
AGBL3 | ENST00000435976.6 | c.775A>C | p.Ile259Leu | missense_variant | 7/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1399364Hom.: 0 Cov.: 30 AF XY: 0.00000145 AC XY: 1AN XY: 690184
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2023 | The c.775A>C (p.I259L) alteration is located in exon 7 (coding exon 6) of the AGBL3 gene. This alteration results from a A to C substitution at nucleotide position 775, causing the isoleucine (I) at amino acid position 259 to be replaced by a leucine (L). 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