rs72809554
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000429.3(MAT1A):c.1085+114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0291 in 1,457,376 control chromosomes in the GnomAD database, including 750 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 0.024 ( 52 hom., cov: 33)
Exomes 𝑓: 0.030 ( 698 hom. )
Consequence
MAT1A
NM_000429.3 intron
NM_000429.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.125
Genes affected
MAT1A (HGNC:6903): (methionine adenosyltransferase 1A) This gene catalyzes a two-step reaction that involves the transfer of the adenosyl moiety of ATP to methionine to form S-adenosylmethionine and tripolyphosphate, which is subsequently cleaved to PPi and Pi. S-adenosylmethionine is the source of methyl groups for most biological methylations. The encoded protein is found as a homotetramer (MAT I) or a homodimer (MAT III) whereas a third form, MAT II (gamma), is encoded by the MAT2A gene. Mutations in this gene are associated with methionine adenosyltransferase deficiency. [provided by RefSeq, Jul 2008]
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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=-0.86).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0244 (3712/152282) while in subpopulation NFE AF= 0.0326 (2219/68030). AF 95% confidence interval is 0.0315. There are 52 homozygotes in gnomad4. There are 1761 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 52 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAT1A | NM_000429.3 | c.1085+114G>A | intron_variant | ENST00000372213.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAT1A | ENST00000372213.8 | c.1085+114G>A | intron_variant | 1 | NM_000429.3 | P1 | |||
MAT1A | ENST00000480845.1 | n.317+114G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
MAT1A | ENST00000485270.5 | n.597+114G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0244 AC: 3713AN: 152164Hom.: 52 Cov.: 33
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GnomAD4 exome AF: 0.0296 AC: 38672AN: 1305094Hom.: 698 AF XY: 0.0291 AC XY: 19133AN XY: 656706
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GnomAD4 genome ? AF: 0.0244 AC: 3712AN: 152282Hom.: 52 Cov.: 33 AF XY: 0.0236 AC XY: 1761AN XY: 74462
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at