chr7-135034207-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_178563.4(AGBL3):c.616C>A(p.Gln206Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,551,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGBL3 | NM_178563.4 | c.616C>A | p.Gln206Lys | missense_variant | Exon 7 of 17 | ENST00000436302.6 | NP_848658.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGBL3 | ENST00000436302.6 | c.616C>A | p.Gln206Lys | missense_variant | Exon 7 of 17 | 2 | NM_178563.4 | ENSP00000388275.2 | ||
AGBL3 | ENST00000275763.10 | n.616C>A | non_coding_transcript_exon_variant | Exon 7 of 17 | 1 | ENSP00000275763.6 | ||||
AGBL3 | ENST00000435976.6 | c.616C>A | p.Gln206Lys | missense_variant | Exon 7 of 16 | 5 | ENSP00000401220.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000641 AC: 1AN: 156080Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82684
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1399290Hom.: 0 Cov.: 30 AF XY: 0.00000145 AC XY: 1AN XY: 690146
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.616C>A (p.Q206K) alteration is located in exon 7 (coding exon 6) of the AGBL3 gene. This alteration results from a C to A substitution at nucleotide position 616, causing the glutamine (Q) at amino acid position 206 to be replaced by a lysine (K). 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