rs10887710

Variant names:

• chr10-80270029-T-C
• rs10887710
• ENST00000871619.1:c.*3752A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-80270029-T-C
• chr10-80270029-T-G

Variant summary

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

The ENST00000871619.1(MAT1A):​c.*3752A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 151,784 control chromosomes in the GnomAD database, including 3,166 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 0.19 (3166 hom., cov: 32)
• Consequence: MAT1A ENST00000871619.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 3 publications found

Genes affected

MAT1A (HGNC:6903): (methionine adenosyltransferase 1A) This gene catalyzes a two-step reaction that involves the transfer of the adenosyl moiety of ATP to methionine to form S-adenosylmethionine and tripolyphosphate, which is subsequently cleaved to PPi and Pi. S-adenosylmethionine is the source of methyl groups for most biological methylations. The encoded protein is found as a homotetramer (MAT I) or a homodimer (MAT III) whereas a third form, MAT II (gamma), is encoded by the MAT2A gene. Mutations in this gene are associated with methionine adenosyltransferase deficiency. [provided by RefSeq, Jul 2008]

MAT1A Gene-Disease associations (from GenCC):

• methionine adenosyltransferase deficiency

  Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, Orphanet, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000871619.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAT1A	ENST00000871619.1		c.*3752A>G		3_prime_UTR	Exon 10 of 10	ENSP00000541678.1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29017 AN: 151666 Hom.: 3172 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.191 AC: 29004 AN: 151784 Hom.: 3166 Cov.: 32 AF XY: 0.195 AC XY: 14435 AN XY: 74148

African (AFR) AF: 0.135 AC: 5582 AN: 41356

American (AMR) AF: 0.211 AC: 3214 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2642 AN: 5154

South Asian (SAS) AF: 0.199 AC: 956 AN: 4808

European-Finnish (FIN) AF: 0.251 AC: 2636 AN: 10512

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12524 AN: 67924

Other (OTH) AF: 0.211 AC: 444 AN: 2100

Alfa AF: 0.189 Hom.: 2772

Bravo AF: 0.189

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10887710; hg19: chr10-82029785;