chr3-49417548-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000481.4(AMT):​c.1204C>T​(p.Leu402Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L402L) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

AMT
NM_000481.4 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.17
Variant links:
Genes affected
AMT (HGNC:473): (aminomethyltransferase) This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23110786).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AMTNM_000481.4 linkuse as main transcriptc.1204C>T p.Leu402Phe missense_variant 9/9 ENST00000273588.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AMTENST00000273588.9 linkuse as main transcriptc.1204C>T p.Leu402Phe missense_variant 9/91 NM_000481.4 P1P48728-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Non-ketotic hyperglycinemia Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingInvitaeSep 27, 2022This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 402 of the AMT protein (p.Leu402Phe). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with AMT-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt AMT protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Uncertain
0.093
D
BayesDel_noAF
Benign
-0.10
CADD
Benign
16
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.52
D;T;.;T;T;T;.;T;.;.
Eigen
Benign
-0.092
Eigen_PC
Benign
-0.13
FATHMM_MKL
Benign
0.75
D
LIST_S2
Uncertain
0.90
D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.059
D
MetaRNN
Benign
0.23
T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.0047
D
MutationAssessor
Benign
1.8
L;.;.;.;.;.;.;.;.;.
MutationTaster
Benign
0.53
D;N;N;N;N
PrimateAI
Benign
0.47
T
PROVEAN
Benign
-0.94
N;.;N;.;.;.;.;.;.;.
REVEL
Benign
0.24
Sift
Benign
0.090
T;.;T;.;.;.;.;.;.;.
Sift4G
Benign
0.17
T;.;T;.;.;.;.;.;.;.
Polyphen
0.85
P;.;.;.;.;.;.;.;.;.
Vest4
0.17
MutPred
0.31
Gain of solvent accessibility (P = 0.0281);.;.;.;.;.;.;.;.;.;
MVP
0.96
MPC
0.26
ClinPred
0.15
T
GERP RS
3.0
Varity_R
0.24
gMVP
0.59

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.

Other links and lift over

dbSNP: rs2049018724; hg19: chr3-49454981; API