chr1-48590895-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032785.4(AGBL4):c.1042C>T(p.Arg348Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,608,334 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R348Q) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL4 | NM_032785.4 | c.1042C>T | p.Arg348Trp | missense_variant | 10/14 | ENST00000371839.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL4 | ENST00000371839.6 | c.1042C>T | p.Arg348Trp | missense_variant | 10/14 | 2 | NM_032785.4 | P1 | |
AGBL4 | ENST00000416121.5 | c.580C>T | p.Arg194Trp | missense_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152040Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000375 AC: 9AN: 240192Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129834
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1456294Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8AN XY: 723566
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152040Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.1042C>T (p.R348W) alteration is located in exon 10 (coding exon 10) of the AGBL4 gene. This alteration results from a C to T substitution at nucleotide position 1042, causing the arginine (R) at amino acid position 348 to be replaced by a tryptophan (W). 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