3-30728348-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_207359.3(GADL1):c.1460G>A(p.Arg487Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,613,850 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207359.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GADL1 | NM_207359.3 | c.1460G>A | p.Arg487Gln | missense_variant | 15/15 | ENST00000282538.10 | |
GADL1 | XM_017006297.2 | c.1403G>A | p.Arg468Gln | missense_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GADL1 | ENST00000282538.10 | c.1460G>A | p.Arg487Gln | missense_variant | 15/15 | 5 | NM_207359.3 | P1 | |
GADL1 | ENST00000498387.1 | n.517G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 39AN: 250916Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135620
GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461564Hom.: 2 Cov.: 31 AF XY: 0.0000798 AC XY: 58AN XY: 727088
GnomAD4 genome AF: 0.000322 AC: 49AN: 152286Hom.: 1 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.1460G>A (p.R487Q) alteration is located in exon 15 (coding exon 15) of the GADL1 gene. This alteration results from a G to A substitution at nucleotide position 1460, causing the arginine (R) at amino acid position 487 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