chr5-163505175-C-T

Variant names:

• chr5-163505175-C-T
• rs28364754
• ENST00000280969.9:c.30+1751C>T

Variant summary

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

The ENST00000280969.9(MAT2B):​c.30+1751C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 151,552 control chromosomes in the GnomAD database, including 100 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 0.031 (100 hom., cov: 32)
• Consequence: MAT2B ENST00000280969.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 0 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2B	NM_182796.2	c.30+1751C>T		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+1751C>T		intron_variant	Intron 1 of 6	1		ENSP00000280969.5
MAT2B	ENST00000694939.1	c.30+1751C>T		intron_variant	Intron 1 of 4			ENSP00000511606.1
MAT2B	ENST00000694940.1	c.-535+1053C>T		intron_variant	Intron 1 of 6			ENSP00000511607.1

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 4697 AN: 151436 Hom.: 99 Cov.: 32

Gnomad AFR AF: 0.00739

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.0294

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

GnomAD4 genome AF: 0.0310 AC: 4703 AN: 151552 Hom.: 100 Cov.: 32 AF XY: 0.0330 AC XY: 2442 AN XY: 74042

African (AFR) AF: 0.00737 AC: 303 AN: 41118

American (AMR) AF: 0.0290 AC: 442 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0256 AC: 89 AN: 3472

East Asian (EAS) AF: 0.0563 AC: 290 AN: 5154

South Asian (SAS) AF: 0.0192 AC: 92 AN: 4800

European-Finnish (FIN) AF: 0.0802 AC: 841 AN: 10492

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0365 AC: 2479 AN: 67968

Other (OTH) AF: 0.0320 AC: 67 AN: 2096

Alfa AF: 0.0349 Hom.: 32

Bravo AF: 0.0289

Asia WGS AF: 0.0620 AC: 216 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-1.1
PromoterAI		0.0038	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs28364754; hg19: chr5-162932181;