chr1-236885376-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000254.3(MTR):c.2775+157G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,086 control chromosomes in the GnomAD database, including 7,550 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.29 ( 7550 hom., cov: 32)
Consequence
MTR
NM_000254.3 intron
NM_000254.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.749
Publications
45 publications found
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 Gene-Disease associations (from GenCC):
- methylcobalamin deficiency type cblGInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 1-236885376-G-T is Benign according to our data. Variant chr1-236885376-G-T is described in ClinVar as Benign. ClinVar VariationId is 1282022.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.290 AC: 44135AN: 151968Hom.: 7532 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
44135
AN:
151968
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.291 AC: 44195AN: 152086Hom.: 7550 Cov.: 32 AF XY: 0.291 AC XY: 21673AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
44195
AN:
152086
Hom.:
Cov.:
32
AF XY:
AC XY:
21673
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
19393
AN:
41440
American (AMR)
AF:
AC:
3535
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
637
AN:
3466
East Asian (EAS)
AF:
AC:
899
AN:
5170
South Asian (SAS)
AF:
AC:
1954
AN:
4820
European-Finnish (FIN)
AF:
AC:
2177
AN:
10580
Middle Eastern (MID)
AF:
AC:
64
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14766
AN:
67998
Other (OTH)
AF:
AC:
566
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1522
3044
4566
6088
7610
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
434
868
1302
1736
2170
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1058
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 01, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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