rs12286721
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024783.4(AGBL2):c.2013G>T(p.Met671Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,587,002 control chromosomes in the GnomAD database, including 253,138 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024783.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGBL2 | NM_024783.4 | c.2013G>T | p.Met671Ile | missense_variant | 13/19 | ENST00000525123.6 | NP_079059.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGBL2 | ENST00000525123.6 | c.2013G>T | p.Met671Ile | missense_variant | 13/19 | 1 | NM_024783.4 | ENSP00000435582.1 | ||
AGBL2 | ENST00000528244.5 | c.1899G>T | p.Met633Ile | missense_variant | 12/16 | 2 | ENSP00000436630.1 |
Frequencies
GnomAD3 genomes AF: 0.594 AC: 89788AN: 151222Hom.: 26979 Cov.: 29
GnomAD3 exomes AF: 0.581 AC: 144818AN: 249432Hom.: 43163 AF XY: 0.568 AC XY: 76574AN XY: 134816
GnomAD4 exome AF: 0.557 AC: 799242AN: 1435662Hom.: 226136 Cov.: 26 AF XY: 0.553 AC XY: 395936AN XY: 715812
GnomAD4 genome AF: 0.594 AC: 89850AN: 151340Hom.: 27002 Cov.: 29 AF XY: 0.600 AC XY: 44315AN XY: 73894
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at