chr1-1020183-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198576.4(AGRN):āc.11G>Cā(p.Arg4Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 1,333,304 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_198576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGRN | NM_198576.4 | c.11G>C | p.Arg4Pro | missense_variant | 1/36 | ENST00000379370.7 | NP_940978.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.11G>C | p.Arg4Pro | missense_variant | 1/36 | 1 | NM_198576.4 | ENSP00000368678 | P1 | |
AGRN | ENST00000620552.4 | c.-404G>C | 5_prime_UTR_variant | 1/39 | 5 | ENSP00000484607 |
Frequencies
GnomAD3 genomes AF: 0.0120 AC: 1806AN: 150674Hom.: 26 Cov.: 31
GnomAD3 exomes AF: 0.000944 AC: 25AN: 26472Hom.: 1 AF XY: 0.000552 AC XY: 9AN XY: 16290
GnomAD4 exome AF: 0.000994 AC: 1176AN: 1182524Hom.: 18 Cov.: 29 AF XY: 0.000842 AC XY: 487AN XY: 578112
GnomAD4 genome AF: 0.0120 AC: 1806AN: 150780Hom.: 26 Cov.: 31 AF XY: 0.0117 AC XY: 859AN XY: 73662
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
AGRN-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 29, 2019 | This variant is classified as 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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at