chr11-47679976-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024783.4(AGBL2):āc.2013G>Cā(p.Met671Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_024783.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGBL2 | NM_024783.4 | c.2013G>C | p.Met671Ile | missense_variant | Exon 13 of 19 | ENST00000525123.6 | NP_079059.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGBL2 | ENST00000525123.6 | c.2013G>C | p.Met671Ile | missense_variant | Exon 13 of 19 | 1 | NM_024783.4 | ENSP00000435582.1 | ||
AGBL2 | ENST00000528244.5 | c.1899G>C | p.Met633Ile | missense_variant | Exon 12 of 16 | 2 | ENSP00000436630.1 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1442050Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 718766
GnomAD4 genome Cov.: 29
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at