chr11-131911606-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001352005.2(NTM):āc.125T>Cā(p.Met42Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000911 in 1,614,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000079 ( 0 hom., cov: 33)
Exomes š: 0.000092 ( 0 hom. )
Consequence
NTM
NM_001352005.2 missense
NM_001352005.2 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 5.82
Genes affected
NTM (HGNC:17941): (neurotrimin) This gene encodes a member of the IgLON (LAMP, OBCAM, Ntm) family of immunoglobulin (Ig) domain-containing glycosylphosphatidylinositol (GPI)-anchored cell adhesion molecules. The encoded protein may promote neurite outgrowth and adhesion via a homophilic mechanism. This gene is closely linked to a related family member, opioid binding protein/cell adhesion molecule-like (OPCML), on chromosome 11. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2009]
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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=0.090693206).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTM | NM_001352005.2 | c.125T>C | p.Met42Thr | missense_variant | 2/9 | ENST00000683400.1 | |
LOC107984413 | XR_007062957.1 | n.1A>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTM | ENST00000683400.1 | c.125T>C | p.Met42Thr | missense_variant | 2/9 | NM_001352005.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251378Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135870
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GnomAD4 exome AF: 0.0000923 AC: 135AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.0000949 AC XY: 69AN XY: 727236
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GnomAD4 genome AF: 0.0000788 AC: 12AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74472
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.125T>C (p.M42T) alteration is located in exon 1 (coding exon 1) of the NTM gene. This alteration results from a T to C substitution at nucleotide position 125, causing the methionine (M) at amino acid position 42 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;.;T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;N;N;N
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
N;D;N;N;N;N
REVEL
Benign
Sift
Benign
T;.;T;T;T;T
Sift4G
Benign
T;.;T;T;T;T
Polyphen
B;.;.;B;B;B
Vest4
MVP
MPC
0.73
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at