13-106559541-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018011.4(ARGLU1):c.464G>A(p.Arg155Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000248 in 1,614,032 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 (★).
Frequency
Consequence
NM_018011.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARGLU1 | NM_018011.4 | c.464G>A | p.Arg155Gln | missense_variant | Exon 2 of 4 | ENST00000400198.8 | NP_060481.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARGLU1 | ENST00000400198.8 | c.464G>A | p.Arg155Gln | missense_variant | Exon 2 of 4 | 1 | NM_018011.4 | ENSP00000383059.3 | ||
ARGLU1 | ENST00000360629.3 | n.168G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 | |||||
ARGLU1 | ENST00000375926.5 | n.237G>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 5 | |||||
ARGLU1 | ENST00000472226.2 | n.682G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249546Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135388
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461882Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.464G>A (p.R155Q) alteration is located in exon 2 (coding exon 2) of the ARGLU1 gene. This alteration results from a G to A substitution at nucleotide position 464, causing the arginine (R) at amino acid position 155 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