rs4869087

Positions:

• chr5-163510219-C-A
• chr5-163510219-C-G
• chr5-163510219-C-T

Variant summary

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

The NM_013283.5(MAT2B):​c.64-1783C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,902 control chromosomes in the GnomAD database, including 30,837 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 0.61 (30837 hom., cov: 31)
• Consequence: MAT2B NM_013283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAT2B	NM_013283.5	c.64-1783C>A		intron_variant		ENST00000321757.11	NP_037415.1
MAT2B	NM_182796.2	c.31-1783C>A		intron_variant			NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000321757.11	c.64-1783C>A		intron_variant		1	NM_013283.5	ENSP00000325425	P1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93385 AN: 151786 Hom.: 30827 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.653

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.615 AC: 93418 AN: 151902 Hom.: 30837 Cov.: 31 AF XY: 0.615 AC XY: 45637 AN XY: 74240

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.645

Alfa AF: 0.672 Hom.: 7149

Bravo AF: 0.612

Asia WGS AF: 0.729 AC: 2533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.30

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: rs4869087; hg19: chr5-162937225;