5-163515148-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013283.5(MAT2B):​c.526+1154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,048 control chromosomes in the GnomAD database, including 18,356 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 0.47 ( 18356 hom., cov: 32)

Consequence

MAT2B
NM_013283.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAT2BNM_013283.5 linkc.526+1154C>T intron_variant Intron 4 of 6 ENST00000321757.11 NP_037415.1 Q9NZL9-1A0A140VJP2
MAT2BNM_182796.2 linkc.493+1154C>T intron_variant Intron 4 of 6 NP_877725.1 Q9NZL9-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAT2BENST00000321757.11 linkc.526+1154C>T intron_variant Intron 4 of 6 1 NM_013283.5 ENSP00000325425.6 Q9NZL9-1

Frequencies

GnomAD3 genomes
AF:
0.472
AC:
71733
AN:
151932
Hom.:
18320
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.669
Gnomad AMI
AF:
0.525
Gnomad AMR
AF:
0.379
Gnomad ASJ
AF:
0.384
Gnomad EAS
AF:
0.202
Gnomad SAS
AF:
0.362
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.420
Gnomad OTH
AF:
0.447
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.472
AC:
71820
AN:
152048
Hom.:
18356
Cov.:
32
AF XY:
0.466
AC XY:
34634
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.669
Gnomad4 AMR
AF:
0.378
Gnomad4 ASJ
AF:
0.384
Gnomad4 EAS
AF:
0.203
Gnomad4 SAS
AF:
0.361
Gnomad4 FIN
AF:
0.382
Gnomad4 NFE
AF:
0.420
Gnomad4 OTH
AF:
0.446
Alfa
AF:
0.457
Hom.:
2097
Bravo
AF:
0.483
Asia WGS
AF:
0.376
AC:
1309
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
3.1
DANN
Benign
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6898075; hg19: chr5-162942154; API