1-1051307-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_198576.4(AGRN):c.5308G>T(p.Asp1770Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000704 in 1,419,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. D1770N) has been classified as Uncertain significance.
Frequency
Consequence
NM_198576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.5308G>T | p.Asp1770Tyr | missense_variant | Exon 31 of 36 | 1 | NM_198576.4 | ENSP00000368678.2 | ||
AGRN | ENST00000651234.1 | c.5005G>T | p.Asp1669Tyr | missense_variant | Exon 31 of 38 | ENSP00000499046.1 | ||||
AGRN | ENST00000652369.1 | c.4993G>T | p.Asp1665Tyr | missense_variant | Exon 30 of 35 | ENSP00000498543.1 | ||||
AGRN | ENST00000620552.4 | c.4906G>T | p.Asp1636Tyr | missense_variant | Exon 32 of 39 | 5 | ENSP00000484607.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.04e-7 AC: 1AN: 1419922Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 702398
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.