rs964945

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-163513733-G-A
• chr5-163513733-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2B	NM_013283.5	c.373+64G>A		intron_variant	Intron 3 of 6	ENST00000321757.11	NP_037415.1
MAT2B	NM_182796.2	c.340+64G>A		intron_variant	Intron 3 of 6		NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000321757.11	c.373+64G>A		intron_variant	Intron 3 of 6	1	NM_013283.5	ENSP00000325425.6

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

Gnomad4 AFR exome AF: 0.972

Gnomad4 AMR exome AF: 0.997

Gnomad4 ASJ exome AF: 0.998

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.997

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

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.996

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.991

Alfa AF: 0.995 Hom.: 9382

Bravo AF: 0.989

Asia WGS AF: 0.998 AC: 3465 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.61
DANN	Benign	0.46

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: rs964945; hg19: chr5-162940739;