rs201073369
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198576.4(AGRN):c.67G>A(p.Val23Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000232 in 1,294,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V23L) has been classified as Likely benign.
Frequency
Consequence
NM_198576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGRN | NM_198576.4 | c.67G>A | p.Val23Ile | 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.67G>A | p.Val23Ile | missense_variant | 1/36 | 1 | NM_198576.4 | ENSP00000368678.2 | ||
AGRN | ENST00000620552 | c.-348G>A | 5_prime_UTR_variant | 1/39 | 5 | ENSP00000484607.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000263 AC: 2AN: 75972Hom.: 0 AF XY: 0.0000230 AC XY: 1AN XY: 43528
GnomAD4 exome AF: 0.00000232 AC: 3AN: 1294070Hom.: 0 Cov.: 32 AF XY: 0.00000471 AC XY: 3AN XY: 637506
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at