1-1050014-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_198576.4(AGRN):c.4856G>T(p.Arg1619Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,607,884 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. R1619H) has been classified as Uncertain significance.
Frequency
Consequence
NM_198576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.4856G>T | p.Arg1619Leu | missense_variant | Exon 27 of 36 | 1 | NM_198576.4 | ENSP00000368678.2 | ||
AGRN | ENST00000651234.1 | c.4541G>T | p.Arg1514Leu | missense_variant | Exon 26 of 38 | ENSP00000499046.1 | ||||
AGRN | ENST00000652369.1 | c.4541G>T | p.Arg1514Leu | missense_variant | Exon 26 of 35 | ENSP00000498543.1 | ||||
AGRN | ENST00000620552.4 | c.4442G>T | p.Arg1481Leu | missense_variant | Exon 27 of 39 | 5 | ENSP00000484607.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152026Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000440 AC: 1AN: 227440Hom.: 0 AF XY: 0.00000796 AC XY: 1AN XY: 125694
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455858Hom.: 0 Cov.: 71 AF XY: 0.00000414 AC XY: 3AN XY: 723898
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152026Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at