chr1-1020204-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198576.4(AGRN):c.32G>T(p.Arg11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000512 in 1,368,114 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. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R11Q) 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_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGRN | NM_198576.4 | c.32G>T | p.Arg11Leu | missense_variant | 1/36 | ENST00000379370.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.32G>T | p.Arg11Leu | missense_variant | 1/36 | 1 | NM_198576.4 | P1 | |
AGRN | ENST00000620552.4 | c.-383G>T | 5_prime_UTR_variant | 1/39 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 4AN: 151164Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000247 AC: 3AN: 1216950Hom.: 0 Cov.: 29 AF XY: 0.00000168 AC XY: 1AN XY: 596600
GnomAD4 genome AF: 0.0000265 AC: 4AN: 151164Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73800
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.32G>T (p.R11L) alteration is located in exon 1 (coding exon 1) of the AGRN gene. This alteration results from a G to T substitution at nucleotide position 32, causing the arginine (R) at amino acid position 11 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at