Variant rs55855057 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000429.3(MAT1A):c.951+44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,544,440 control chromosomes in the GnomAD database, including 13,785 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 0.10 ( 1028 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12757 hom. )

Consequence

MAT1A
NM_000429.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.490

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAT1A	NM_000429.3 linkuse as main transcript	c.951+44C>T		intron_variant		ENST00000372213.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
MAT1A	ENST00000372213.8 linkuse as main transcript	c.951+44C>T	intron_variant	1	NM_000429.3	P1
MAT1A	ENST00000480845.1 linkuse as main transcript	n.183+44C>T	intron_variant, non_coding_transcript_variant	3
MAT1A	ENST00000485270.5 linkuse as main transcript	n.463+44C>T	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15603

AN:

152114

Hom.:

1015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.0177

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.0727

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.115

GnomAD3 exomes

AF:

0.142

AC:

21825

AN:

153890

Hom.:

2082

AF XY:

0.146

AC XY:

11826

AN XY:

81260

show subpopulations

Gnomad AFR exome

AF:

0.0430

Gnomad AMR exome

AF:

0.250

Gnomad ASJ exome

AF:

0.100

Gnomad EAS exome

AF:

0.0135

Gnomad SAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.0792

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.141

GnomAD4 exome

AF:

0.128

AC:

178080

AN:

1392208

Hom.:

12757

Cov.:

AF XY:

0.131

AC XY:

89711

AN XY:

686924

show subpopulations

Gnomad4 AFR exome

AF:

0.0382

Gnomad4 AMR exome

AF:

0.243

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.0209

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.0816

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.103

AC:

15642

AN:

152232

Hom.:

1028

Cov.:

AF XY:

0.104

AC XY:

7736

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0429

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.0178

Gnomad4 SAS

AF:

0.243

Gnomad4 FIN

AF:

0.0727

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.119

Alfa

AF:

0.115

Hom.:

199

Bravo

AF:

0.106

Asia WGS

AF:

0.149

AC:

521

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.5

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over