chr5-163518263-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_013283.5(MAT2B):c.905C>T(p.Thr302Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000769 in 1,613,928 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00095 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00075 ( 13 hom. )
Consequence
MAT2B
NM_013283.5 missense
NM_013283.5 missense
Scores
3
13
Clinical Significance
Conservation
PhyloP100: 0.870
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005980402).
BP6
?
Variant 5-163518263-C-T is Benign according to our data. Variant chr5-163518263-C-T is described in ClinVar as [Benign]. Clinvar id is 717327.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000946 (144/152268) while in subpopulation EAS AF= 0.0212 (110/5180). AF 95% confidence interval is 0.018. There are 2 homozygotes in gnomad4. There are 58 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAT2B | NM_013283.5 | c.905C>T | p.Thr302Ile | missense_variant | 7/7 | ENST00000321757.11 | |
MAT2B | NM_182796.2 | c.872C>T | p.Thr291Ile | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAT2B | ENST00000321757.11 | c.905C>T | p.Thr302Ile | missense_variant | 7/7 | 1 | NM_013283.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000946 AC: 144AN: 152152Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00188 AC: 472AN: 251222Hom.: 3 AF XY: 0.00172 AC XY: 234AN XY: 135782
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GnomAD4 exome AF: 0.000751 AC: 1097AN: 1461660Hom.: 13 Cov.: 30 AF XY: 0.000755 AC XY: 549AN XY: 727126
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
0.42
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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