rs779516004
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_198576.4(AGRN):c.3752-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000099 in 1,576,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_198576.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGRN | NM_198576.4 | c.3752-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000379370.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGRN | ENST00000379370.7 | c.3752-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_198576.4 | P1 | |||
AGRN | ENST00000620552.4 | c.3338-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
AGRN | ENST00000651234.1 | c.3437-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||||
AGRN | ENST00000652369.1 | c.3437-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000178 AC: 33AN: 184916Hom.: 0 AF XY: 0.000227 AC XY: 23AN XY: 101412
GnomAD4 exome AF: 0.000103 AC: 147AN: 1424294Hom.: 0 Cov.: 36 AF XY: 0.000106 AC XY: 75AN XY: 705670
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 12, 2015 | - - |
Congenital myasthenic syndrome 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at