1-48539690-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032785.4(AGBL4):c.1316G>A(p.Arg439Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,543,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032785.4 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 |
---|---|---|---|---|---|---|---|
AGBL4 | NM_032785.4 | c.1316G>A | p.Arg439Gln | missense_variant | 12/14 | ENST00000371839.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL4 | ENST00000371839.6 | c.1316G>A | p.Arg439Gln | missense_variant | 12/14 | 2 | NM_032785.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000325 AC: 5AN: 153760Hom.: 0 AF XY: 0.0000369 AC XY: 3AN XY: 81252
GnomAD4 exome AF: 0.0000280 AC: 39AN: 1391854Hom.: 0 Cov.: 30 AF XY: 0.0000321 AC XY: 22AN XY: 686032
GnomAD4 genome AF: 0.0000526 AC: 8AN: 151994Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.1316G>A (p.R439Q) alteration is located in exon 12 (coding exon 12) of the AGBL4 gene. This alteration results from a G to A substitution at nucleotide position 1316, causing the arginine (R) at amino acid position 439 to be replaced by a glutamine (Q). 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