5-163513733-G-A

Variant names:

• chr5-163513733-G-A
• rs964945
• NM_013283.5:c.373+64G>A

Variant summary

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

The NM_013283.5(MAT2B):​c.373+64G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.998 in 1,526,496 control chromosomes in the GnomAD database, including 760,500 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 0.99 (74780 hom., cov: 34)
  • Exomes 𝑓: 1.0 (685720 hom.)
• Consequence: MAT2B NM_013283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT2B	NM_013283.5	MANE Select	c.373+64G>A		intron	N/A	NP_037415.1
	MAT2B	NM_182796.2		c.340+64G>A		intron	N/A	NP_877725.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT2B	ENST00000321757.11	TSL:1 MANE Select	c.373+64G>A		intron	N/A	ENSP00000325425.6
	MAT2B	ENST00000280969.9	TSL:1	c.340+64G>A		intron	N/A	ENSP00000280969.5
	MAT2B	ENST00000518095.5	TSL:1	c.373+64G>A		intron	N/A	ENSP00000428046.1

Frequencies

GnomAD3 genomes AF: 0.991 AC: 150839 AN: 152254 Hom.: 74733 Cov.: 34

Gnomad AFR AF: 0.969

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.991

GnomAD4 exome AF: 0.999 AC: 1372763 AN: 1374124 Hom.: 685720 Cov.: 19 AF XY: 0.999 AC XY: 685936 AN XY: 686536

African (AFR) AF: 0.972 AC: 29910 AN: 30786

American (AMR) AF: 0.997 AC: 40335 AN: 40456

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 24730 AN: 24786

East Asian (EAS) AF: 1.00 AC: 39034 AN: 39034

South Asian (SAS) AF: 1.00 AC: 81557 AN: 81564

European-Finnish (FIN) AF: 1.00 AC: 52795 AN: 52796

Middle Eastern (MID) AF: 0.997 AC: 5461 AN: 5478

European-Non Finnish (NFE) AF: 1.00 AC: 1042012 AN: 1042130

Other (OTH) AF: 0.997 AC: 56929 AN: 57094

GnomAD4 genome AF: 0.991 AC: 150945 AN: 152372 Hom.: 74780 Cov.: 34 AF XY: 0.991 AC XY: 73826 AN XY: 74510

African (AFR) AF: 0.968 AC: 40273 AN: 41586

American (AMR) AF: 0.996 AC: 15245 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3462 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5186

South Asian (SAS) AF: 1.00 AC: 4827 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10620 AN: 10620

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68031 AN: 68048

Other (OTH) AF: 0.991 AC: 2097 AN: 2116

Alfa AF: 0.994 Hom.: 9744

Bravo AF: 0.989

Asia WGS AF: 0.998 AC: 3465 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.61
DANN	Benign	0.46
PhyloP100		-0.14
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: rs964945; hg19: chr5-162940739;