5-163504712-T-C

Variant names:

• chr5-163504712-T-C
• rs7734424
• ENST00000280969.9:c.30+1288T>C

Variant summary

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

The NM_182796.2(MAT2B):​c.30+1288T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,238 control chromosomes in the GnomAD database, including 52,210 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 0.83 (52210 hom., cov: 32)
• Consequence: MAT2B NM_182796.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2B	NM_182796.2	c.30+1288T>C		intron_variant	Intron 1 of 6		NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000280969.9	c.30+1288T>C		intron_variant	Intron 1 of 6	1		ENSP00000280969.5
MAT2B	ENST00000694939.1	c.30+1288T>C		intron_variant	Intron 1 of 4			ENSP00000511606.1
MAT2B	ENST00000694940.1	c.-535+590T>C		intron_variant	Intron 1 of 6			ENSP00000511607.1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125761 AN: 152120 Hom.: 52180 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.827 AC: 125844 AN: 152238 Hom.: 52210 Cov.: 32 AF XY: 0.826 AC XY: 61462 AN XY: 74438

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.831

Alfa AF: 0.827 Hom.: 12763

Bravo AF: 0.829

Asia WGS AF: 0.850 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.83
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7734424; hg19: chr5-162931718;