5-163517402-A-G

Position:

• chr5-163517402-A-G

Variant summary

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

The ENST00000518095.5(MAT2B):​c.*631A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 443,972 control chromosomes in the GnomAD database, including 50,661 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 0.40 (14019 hom., cov: 32)
  • Exomes 𝑓: 0.49 (36642 hom.)
• Consequence: MAT2B ENST00000518095.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAT2B	NM_013283.5	c.721-159A>G		intron_variant		ENST00000321757.11	NP_037415.1
MAT2B	NM_182796.2	c.688-159A>G		intron_variant			NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000321757.11	c.721-159A>G		intron_variant		1	NM_013283.5	ENSP00000325425	P1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59647 AN: 150862 Hom.: 14016 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.485 AC: 142200 AN: 292988 Hom.: 36642 Cov.: 3 AF XY: 0.487 AC XY: 74418 AN XY: 152900

Gnomad4 AFR exome AF: 0.134

Gnomad4 AMR exome AF: 0.549

Gnomad4 ASJ exome AF: 0.504

Gnomad4 EAS exome AF: 0.759

Gnomad4 SAS exome AF: 0.473

Gnomad4 FIN exome AF: 0.477

Gnomad4 NFE exome AF: 0.464

Gnomad4 OTH exome AF: 0.460

GnomAD4 genome AF: 0.395 AC: 59646 AN: 150984 Hom.: 14019 Cov.: 32 AF XY: 0.401 AC XY: 29578 AN XY: 73790

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.425

Alfa AF: 0.461 Hom.: 25276

Bravo AF: 0.384

Asia WGS AF: 0.523 AC: 1819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.32

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

Other links and lift over

dbSNP: rs4869089; hg19: chr5-162944408;