rs768527925
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_198576.4(AGRN):āc.384C>Gā(p.His128Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,613,288 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H128R) has been classified as Uncertain significance.
Frequency
Consequence
NM_198576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGRN | NM_198576.4 | c.384C>G | p.His128Gln | missense_variant | 2/36 | ENST00000379370.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.384C>G | p.His128Gln | missense_variant | 2/36 | 1 | NM_198576.4 | P1 | |
AGRN | ENST00000620552.4 | c.-31C>G | 5_prime_UTR_variant | 2/39 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000857 AC: 215AN: 250776Hom.: 0 AF XY: 0.000656 AC XY: 89AN XY: 135730
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461050Hom.: 1 Cov.: 33 AF XY: 0.000144 AC XY: 105AN XY: 726802
GnomAD4 genome AF: 0.000145 AC: 22AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74378
ClinVar
Submissions by phenotype
AGRN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 31, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Congenital myasthenic syndrome 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at