rs11580170
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024758.5(AGMAT):c.419G>A(p.Arg140Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,613,544 control chromosomes in the GnomAD database, including 56,087 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024758.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGMAT | NM_024758.5 | c.419G>A | p.Arg140Gln | missense_variant | 2/7 | ENST00000375826.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGMAT | ENST00000375826.4 | c.419G>A | p.Arg140Gln | missense_variant | 2/7 | 1 | NM_024758.5 | P1 | |
DNAJC16 | ENST00000483270.1 | n.2726+7777C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.321 AC: 48690AN: 151784Hom.: 9237 Cov.: 31
GnomAD3 exomes AF: 0.242 AC: 60937AN: 251288Hom.: 8600 AF XY: 0.241 AC XY: 32728AN XY: 135828
GnomAD4 exome AF: 0.246 AC: 359591AN: 1461642Hom.: 46823 Cov.: 44 AF XY: 0.245 AC XY: 178308AN XY: 727130
GnomAD4 genome AF: 0.321 AC: 48755AN: 151902Hom.: 9264 Cov.: 31 AF XY: 0.318 AC XY: 23577AN XY: 74224
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at