rs527639453
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_198576.4(AGRN):c.6119G>A(p.Arg2040Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,548,844 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198576.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGRN | NM_198576.4 | c.6119G>A | p.Arg2040Gln | missense_variant | 36/36 | ENST00000379370.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.6119G>A | p.Arg2040Gln | missense_variant | 36/36 | 1 | NM_198576.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152200Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000447 AC: 68AN: 152046Hom.: 0 AF XY: 0.000517 AC XY: 42AN XY: 81204
GnomAD4 exome AF: 0.000193 AC: 269AN: 1396526Hom.: 1 Cov.: 39 AF XY: 0.000269 AC XY: 185AN XY: 688984
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152318Hom.: 0 Cov.: 34 AF XY: 0.000161 AC XY: 12AN XY: 74476
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at