NM_005911.6:c.-92A>T

Variant names:

• chr2-85539196-A-T
• rs17026419
• NM_005911.6:c.-92A>T

Variant summary

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

The NM_005911.6(MAT2A):​c.-92A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000133 in 751,094 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 0.0000013 (0 hom.)
• Consequence: MAT2A NM_005911.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 0 publications found

Genes affected

MAT2A (HGNC:6904): (methionine adenosyltransferase 2A) The protein encoded by this gene catalyzes the production of S-adenosylmethionine (AdoMet) from methionine and ATP. AdoMet is the key methyl donor in cellular processes. [provided by RefSeq, Jun 2011]

PARTICL (HGNC:50886): (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA)

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=-0.74).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005911.6. 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
	MAT2A	NM_005911.6	MANE Select	c.-92A>T		5_prime_UTR	Exon 1 of 9	NP_005902.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT2A	ENST00000306434.8	TSL:1 MANE Select	c.-92A>T		5_prime_UTR	Exon 1 of 9	ENSP00000303147.3
	MAT2A	ENST00000881374.1		c.-92A>T		5_prime_UTR	Exon 1 of 9	ENSP00000551433.1
	MAT2A	ENST00000881376.1		c.-92A>T		5_prime_UTR	Exon 1 of 9	ENSP00000551435.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000133 AC: 1 AN: 751094 Hom.: 0 Cov.: 10 AF XY: 0.00000256 AC XY: 1 AN XY: 390980

African (AFR) AF: 0.00 AC: 0 AN: 16980

American (AMR) AF: 0.00 AC: 0 AN: 30122

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18786

East Asian (EAS) AF: 0.0000345 AC: 1 AN: 28946

South Asian (SAS) AF: 0.00 AC: 0 AN: 61376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47246

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4004

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 507556

Other (OTH) AF: 0.00 AC: 0 AN: 36078

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.56
PromoterAI		0.11	Neutral

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

Other links and lift over

dbSNP: rs17026419; hg19: chr2-85766319;