6-151468220-T-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024573.3(ARMT1):c.559-123T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 620,922 control chromosomes in the GnomAD database, including 75,907 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.54 ( 25057 hom., cov: 33)
Exomes 𝑓: 0.45 ( 50850 hom. )
Consequence
ARMT1
NM_024573.3 intron
NM_024573.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0800
Genes affected
ARMT1 (HGNC:17872): (acidic residue methyltransferase 1) Enables S-adenosylmethionine-dependent methyltransferase activity; enzyme binding activity; and protein carboxyl O-methyltransferase activity. Involved in methylation and regulation of response to DNA damage stimulus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMT1 | ENST00000367294.4 | c.559-123T>G | intron_variant | Intron 4 of 4 | 1 | NM_024573.3 | ENSP00000356263.3 | |||
ARMT1 | ENST00000545879.5 | c.202-123T>G | intron_variant | Intron 3 of 3 | 2 | ENSP00000444121.1 | ||||
ARMT1 | ENST00000494826.1 | n.*282-123T>G | intron_variant | Intron 3 of 3 | 2 | ENSP00000435882.1 |
Frequencies
GnomAD3 genomes AF: 0.542 AC: 82360AN: 151990Hom.: 25003 Cov.: 33
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GnomAD4 exome AF: 0.451 AC: 211475AN: 468814Hom.: 50850 AF XY: 0.452 AC XY: 111735AN XY: 246962
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GnomAD4 genome AF: 0.542 AC: 82467AN: 152108Hom.: 25057 Cov.: 33 AF XY: 0.544 AC XY: 40450AN XY: 74354
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at