rs7733775

Variant names:

• chr5-163517703-A-G
• rs7733775
• ENST00000518095.5:c.*932A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-163517703-A-G
• chr5-163517703-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518095.5(MAT2B):​c.*932A>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 0.583 in 1,335,750 control chromosomes in the GnomAD database, including 232,507 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 0.50 (21473 hom., cov: 32)
  • Exomes 𝑓: 0.59 (211034 hom.)
• Consequence: MAT2B ENST00000518095.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2B	NM_013283.5	c.834+29A>G		intron_variant	Intron 6 of 6	ENST00000321757.11	NP_037415.1
MAT2B	NM_182796.2	c.801+29A>G		intron_variant	Intron 6 of 6		NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000321757.11	c.834+29A>G		intron_variant	Intron 6 of 6	1	NM_013283.5	ENSP00000325425.6

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76361 AN: 151930 Hom.: 21468 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.533

GnomAD2 exomes AF: 0.602 AC: 148951 AN: 247536 AF XY: 0.605

Gnomad AFR exome AF: 0.242

Gnomad AMR exome AF: 0.674

Gnomad ASJ exome AF: 0.618

Gnomad EAS exome AF: 0.815

Gnomad FIN exome AF: 0.617

Gnomad NFE exome AF: 0.578

Gnomad OTH exome AF: 0.595

GnomAD4 exome AF: 0.593 AC: 702299 AN: 1183702 Hom.: 211034 Cov.: 16 AF XY: 0.596 AC XY: 359420 AN XY: 602768

African (AFR) AF: 0.237 AC: 6543 AN: 27632

American (AMR) AF: 0.669 AC: 29467 AN: 44016

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 14995 AN: 24264

East Asian (EAS) AF: 0.796 AC: 30548 AN: 38394

South Asian (SAS) AF: 0.648 AC: 52180 AN: 80484

European-Finnish (FIN) AF: 0.611 AC: 32444 AN: 53080

Middle Eastern (MID) AF: 0.560 AC: 2937 AN: 5248

European-Non Finnish (NFE) AF: 0.586 AC: 503493 AN: 859448

Other (OTH) AF: 0.581 AC: 29692 AN: 51136

GnomAD4 genome AF: 0.502 AC: 76374 AN: 152048 Hom.: 21473 Cov.: 32 AF XY: 0.509 AC XY: 37862 AN XY: 74330

African (AFR) AF: 0.241 AC: 10009 AN: 41482

American (AMR) AF: 0.608 AC: 9295 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2128 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4180 AN: 5172

South Asian (SAS) AF: 0.637 AC: 3067 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6555 AN: 10558

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39413 AN: 67960

Other (OTH) AF: 0.534 AC: 1128 AN: 2114

Alfa AF: 0.529 Hom.: 7747

Bravo AF: 0.487

Asia WGS AF: 0.624 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.77
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7733775; hg19: chr5-162944709; COSMIC: COSV55200220; COSMIC: COSV55200220;