5-163517402-A-T

Variant names:

• chr5-163517402-A-T
• rs4869089
• ENST00000518095.5:c.*631A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000518095.5(MAT2B):​c.*631A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAT2B ENST00000518095.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 2 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518095.5. 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.721-159A>T		intron	N/A	NP_037415.1
	MAT2B	NM_182796.2		c.688-159A>T		intron	N/A	NP_877725.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT2B	ENST00000518095.5	TSL:1	c.*631A>T		3_prime_UTR	Exon 5 of 5	ENSP00000428046.1
	MAT2B	ENST00000321757.11	TSL:1 MANE Select	c.721-159A>T		intron	N/A	ENSP00000325425.6
	MAT2B	ENST00000280969.9	TSL:1	c.688-159A>T		intron	N/A	ENSP00000280969.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 294082 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 153494

African (AFR) AF: 0.00 AC: 0 AN: 10176

American (AMR) AF: 0.00 AC: 0 AN: 13818

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9492

East Asian (EAS) AF: 0.00 AC: 0 AN: 25858

South Asian (SAS) AF: 0.00 AC: 0 AN: 17228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24670

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1306

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 174218

Other (OTH) AF: 0.00 AC: 0 AN: 17316

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 59981

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		-0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4869089; hg19: chr5-162944408;