chr1-236826841-G-A

Position:

chr1-236826841-G-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2

The NM_000254.3(MTR):c.940G>A(p.Asp314Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0202 in 1,613,906 control chromosomes in the GnomAD database, including 448 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 29 hom., cov: 32)

Exomes 𝑓: 0.020 ( 419 hom. )

Consequence

MTR
NM_000254.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 4.10

Variant links:

Genes affected

MTR (HGNC:7468): (5-methyltetrahydrofolate-homocysteine methyltransferase) This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying cause of methylcobalamin deficiency complementation group G. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]

MTR links:

MTR (HGNC:):

MTR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2

Missense variant in gene, where missense usually causes diseases (based on misZ statistic), MTR. . Gene score misZ 2.0433 (greater than the threshold 3.09). Trascript score misZ 3.2999 (greater than threshold 3.09). GenCC has associacion of gene with methylcobalamin deficiency type cblG.

BP4

Computational evidence support a benign effect (MetaRNN=0.009125441).

BP6

Variant 1-236826841-G-A is Benign according to our data. Variant chr1-236826841-G-A is described in ClinVar as [Benign]. Clinvar id is 296556.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-236826841-G-A is described in Lovd as [Benign]. Variant chr1-236826841-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0181 (2761/152262) while in subpopulation NFE AF= 0.0235 (1599/68024). AF 95% confidence interval is 0.0225. There are 29 homozygotes in gnomad4. There are 1290 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTR	NM_000254.3 linkuse as main transcript	c.940G>A	p.Asp314Asn	missense_variant	11/33	ENST00000366577.10	NP_000245.2	Q99707-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTR	ENST00000366577.10 linkuse as main transcript	c.940G>A	p.Asp314Asn	missense_variant	11/33	1	NM_000254.3	ENSP00000355536.5		Q99707-1

Frequencies

GnomAD3 genomes

AF:

0.0182

AC:

2762

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00927

Gnomad AMI

AF:

0.0736

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.0507

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00393

Gnomad FIN

AF:

0.0137

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0235

Gnomad OTH

AF:

0.0282

GnomAD3 exomes

AF:

0.0186

AC:

4682

AN:

251400

Hom.:

AF XY:

0.0185

AC XY:

2508

AN XY:

135868

show subpopulations

Gnomad AFR exome

AF:

0.00800

Gnomad AMR exome

AF:

0.0152

Gnomad ASJ exome

AF:

0.0491

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00490

Gnomad FIN exome

AF:

0.0158

Gnomad NFE exome

AF:

0.0255

Gnomad OTH exome

AF:

0.0233

GnomAD4 exome

AF:

0.0204

AC:

29802

AN:

1461644

Hom.:

419

Cov.:

AF XY:

0.0200

AC XY:

14518

AN XY:

727162

show subpopulations

Gnomad4 AFR exome

AF:

0.00950

Gnomad4 AMR exome

AF:

0.0163

Gnomad4 ASJ exome

AF:

0.0529

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00546

Gnomad4 FIN exome

AF:

0.0145

Gnomad4 NFE exome

AF:

0.0221

Gnomad4 OTH exome

AF:

0.0214

GnomAD4 genome

AF:

0.0181

AC:

2761

AN:

152262

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1290

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00927

Gnomad4 AMR

AF:

0.0193

Gnomad4 ASJ

AF:

0.0507

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00394

Gnomad4 FIN

AF:

0.0137

Gnomad4 NFE

AF:

0.0235

Gnomad4 OTH

AF:

0.0279

Alfa

AF:

0.0232

Hom.:

Bravo

AF:

0.0187

TwinsUK

AF:

0.0245

AC:

ALSPAC

AF:

0.0218

AC:

ESP6500AA

AF:

0.00817

AC:

ESP6500EA

AF:

0.0262

AC:

225

ExAC

AF:

0.0191

AC:

2317

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.0258

EpiControl

AF:

0.0257

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 25, 2023	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 29, 2016

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Disorders of Intracellular Cobalamin Metabolism

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Methylcobalamin deficiency type cblG

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.13

.;T

Eigen

Benign

-0.15

Eigen_PC

Benign

-0.041

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.94

D;D

MetaRNN

Benign

0.0091

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.8

L;L

PrimateAI

Uncertain

0.52

PROVEAN

Uncertain

-2.5

D;N

REVEL

Benign

0.12

Sift

Benign

0.20

T;T

Sift4G

Benign

0.25

T;T

Polyphen

0.23

.;B

Vest4

0.18

MPC

0.43

ClinPred

0.025

GERP RS

3.1

Varity_R

0.12

gMVP

0.80

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over