5-163515148-C-T

Variant names:

• chr5-163515148-C-T
• rs6898075
• NM_013283.5:c.526+1154C>T

Variant summary

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

The NM_013283.5(MAT2B):​c.526+1154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,048 control chromosomes in the GnomAD database, including 18,356 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 0.47 (18356 hom., cov: 32)
• Consequence: MAT2B NM_013283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2B	NM_013283.5	c.526+1154C>T		intron_variant	Intron 4 of 6	ENST00000321757.11	NP_037415.1
MAT2B	NM_182796.2	c.493+1154C>T		intron_variant	Intron 4 of 6		NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000321757.11	c.526+1154C>T		intron_variant	Intron 4 of 6	1	NM_013283.5	ENSP00000325425.6

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71733 AN: 151932 Hom.: 18320 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.472 AC: 71820 AN: 152048 Hom.: 18356 Cov.: 32 AF XY: 0.466 AC XY: 34634 AN XY: 74304

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.446

Alfa AF: 0.457 Hom.: 2097

Bravo AF: 0.483

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.62

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: rs6898075; hg19: chr5-162942154;