rs7729611
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_013283.5(MAT2B):c.373+70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,511,098 control chromosomes in the GnomAD database, including 68 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 0.012 ( 39 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 29 hom. )
Consequence
MAT2B
NM_013283.5 intron
NM_013283.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.16
Genes affected
MAT2B (HGNC:6905): (methionine adenosyltransferase 2 non-catalytic beta subunit) The protein encoded by this gene belongs to the methionine adenosyltransferase (MAT) family. MAT catalyzes the biosynthesis of S-adenosylmethionine from methionine and ATP. This protein is the regulatory beta subunit of MAT. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]
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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).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0119 (1814/152280) while in subpopulation AFR AF= 0.0416 (1730/41562). AF 95% confidence interval is 0.04. There are 39 homozygotes in gnomad4. There are 865 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 39 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAT2B | NM_013283.5 | c.373+70G>A | intron_variant | ENST00000321757.11 | |||
MAT2B | NM_182796.2 | c.340+70G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAT2B | ENST00000321757.11 | c.373+70G>A | intron_variant | 1 | NM_013283.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0119 AC: 1812AN: 152162Hom.: 39 Cov.: 33
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GnomAD4 exome AF: 0.00119 AC: 1623AN: 1358818Hom.: 29 Cov.: 20 AF XY: 0.00103 AC XY: 699AN XY: 679486
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GnomAD4 genome ? AF: 0.0119 AC: 1814AN: 152280Hom.: 39 Cov.: 33 AF XY: 0.0116 AC XY: 865AN 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