2-85539159-C-G

Position:

• chr2-85539159-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0235 in 684,296 control chromosomes in the GnomAD database, including 262 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 0.021 (60 hom., cov: 33)
  • Exomes 𝑓: 0.024 (202 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0213 (3248/152134) while in subpopulation NFE AF= 0.0326 (2213/67974). AF 95% confidence interval is 0.0314. There are 60 homozygotes in gnomad4. There are 1578 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 60 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85539159C>G		intergenic_region
MAT2A	NM_005911.6	c.-129C>G		upstream_gene_variant		ENST00000306434.8	NP_005902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAT2A	ENST00000306434.8	c.-129C>G		upstream_gene_variant		1	NM_005911.6	ENSP00000303147.3
MAT2A	ENST00000465151.5	n.-9C>G		upstream_gene_variant		2
MAT2A	ENST00000469221.5	n.-9C>G		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3248 AN: 152020 Hom.: 60 Cov.: 33

Gnomad AFR AF: 0.00633

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00973

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.0326

Gnomad OTH AF: 0.0335

GnomAD4 exome AF: 0.0241 AC: 12805 AN: 532162 Hom.: 202 Cov.: 7 AF XY: 0.0237 AC XY: 6666 AN XY: 281224

Gnomad4 AFR exome AF: 0.00625

Gnomad4 AMR exome AF: 0.0212

Gnomad4 ASJ exome AF: 0.0152

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0105

Gnomad4 FIN exome AF: 0.0130

Gnomad4 NFE exome AF: 0.0303

Gnomad4 OTH exome AF: 0.0251

GnomAD4 genome AF: 0.0213 AC: 3248 AN: 152134 Hom.: 60 Cov.: 33 AF XY: 0.0212 AC XY: 1578 AN XY: 74388

Gnomad4 AFR AF: 0.00633

Gnomad4 AMR AF: 0.0308

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00932

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.0326

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.00624 Hom.: 1

Bravo AF: 0.0213

Asia WGS AF: 0.00520 AC: 20 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2028106; hg19: chr2-85766282;