rs10515862

Variant names:

• chr5-163513285-A-G
• rs10515862
• NM_013283.5:c.259-270A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013283.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT2B	NM_013283.5	MANE Select	c.259-270A>G		intron	N/A	NP_037415.1
	MAT2B	NM_182796.2		c.226-270A>G		intron	N/A	NP_877725.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT2B	ENST00000321757.11	TSL:1 MANE Select	c.259-270A>G		intron	N/A	ENSP00000325425.6
	MAT2B	ENST00000280969.9	TSL:1	c.226-270A>G		intron	N/A	ENSP00000280969.5
	MAT2B	ENST00000518095.5	TSL:1	c.259-270A>G		intron	N/A	ENSP00000428046.1

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

African (AFR) AF: 0.00847 AC: 38 AN: 4488

American (AMR) AF: 0.0513 AC: 327 AN: 6370

Ashkenazi Jewish (ASJ) AF: 0.0224 AC: 100 AN: 4456

East Asian (EAS) AF: 0.0846 AC: 802 AN: 9476

South Asian (SAS) AF: 0.0189 AC: 281 AN: 14830

European-Finnish (FIN) AF: 0.0432 AC: 265 AN: 6132

Middle Eastern (MID) AF: 0.0308 AC: 18 AN: 584

European-Non Finnish (NFE) AF: 0.0364 AC: 3235 AN: 88784

Other (OTH) AF: 0.0299 AC: 248 AN: 8292

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

African (AFR) AF: 0.00835 AC: 347 AN: 41566

American (AMR) AF: 0.0350 AC: 535 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3470

East Asian (EAS) AF: 0.0705 AC: 366 AN: 5194

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4832

European-Finnish (FIN) AF: 0.0458 AC: 487 AN: 10624

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2619 AN: 68016

Other (OTH) AF: 0.0350 AC: 74 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.3
DANN	Benign	0.38
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs10515862; hg19: chr5-162940291;