rs10515862

chr5-163513285-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013283.5(MAT2B):c.259-270A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 295,730 control chromosomes in the GnomAD database, including 231 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 0.031 (102 hom., cov: 33)
  • Exomes 𝑓: 0.037 (129 hom.)
• Consequence: MAT2B NM_013283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAT2B	NM_013283.5	c.259-270A>G		intron_variant		ENST00000321757.11
MAT2B	NM_182796.2	c.226-270A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAT2B	ENST00000321757.11	c.259-270A>G		intron_variant		1	NM_013283.5	P1

Frequencies

GnomAD3 genomes AF: 0.0309 AC: 4702 AN: 152200 Hom.: 102 Cov.: 33

Gnomad AFR AF: 0.00837

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0325

GnomAD4 exome AF: 0.0371 AC: 5314 AN: 143412 Hom.: 129 Cov.: 0 AF XY: 0.0356 AC XY: 2701 AN XY: 75768

Gnomad4 AFR exome AF: 0.00847

Gnomad4 AMR exome AF: 0.0513

Gnomad4 ASJ exome AF: 0.0224

Gnomad4 EAS exome AF: 0.0846

Gnomad4 SAS exome AF: 0.0189

Gnomad4 FIN exome AF: 0.0432

Gnomad4 NFE exome AF: 0.0364

Gnomad4 OTH exome AF: 0.0299

GnomAD4 genome AF: 0.0309 AC: 4706 AN: 152318 Hom.: 102 Cov.: 33 AF XY: 0.0313 AC XY: 2335 AN XY: 74492

Gnomad4 AFR AF: 0.00835

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0385

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0364 Hom.: 24

Bravo AF: 0.0318

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.3
Dann	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs10515862; hg19: chr5-162940291;