chr7-135034177-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_178563.4(AGBL3):c.586C>T(p.Arg196Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000406 in 1,550,074 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGBL3 | NM_178563.4 | c.586C>T | p.Arg196Cys | 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.586C>T | p.Arg196Cys | missense_variant | Exon 7 of 17 | 2 | NM_178563.4 | ENSP00000388275.2 | ||
AGBL3 | ENST00000275763.10 | n.586C>T | non_coding_transcript_exon_variant | Exon 7 of 17 | 1 | ENSP00000275763.6 | ||||
AGBL3 | ENST00000435976.6 | c.586C>T | p.Arg196Cys | missense_variant | Exon 7 of 16 | 5 | ENSP00000401220.2 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000194 AC: 3AN: 154732Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 81920
GnomAD4 exome AF: 0.0000236 AC: 33AN: 1397834Hom.: 0 Cov.: 29 AF XY: 0.0000218 AC XY: 15AN XY: 689326
GnomAD4 genome AF: 0.000197 AC: 30AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.586C>T (p.R196C) alteration is located in exon 7 (coding exon 6) of the AGBL3 gene. This alteration results from a C to T substitution at nucleotide position 586, causing the arginine (R) at amino acid position 196 to be replaced by a cysteine (C). 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