chr11-131945450-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001352005.2(NTM):c.167+33802T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,984 control chromosomes in the GnomAD database, including 8,882 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 0.33 ( 8882 hom., cov: 32)
Consequence
NTM
NM_001352005.2 intron
NM_001352005.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.16
Publications
6 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTM | NM_001352005.2 | c.167+33802T>G | intron_variant | Intron 2 of 8 | ENST00000683400.1 | NP_001338934.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.334 AC: 50651AN: 151866Hom.: 8873 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
50651
AN:
151866
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: 0.334 AC: 50713AN: 151984Hom.: 8882 Cov.: 32 AF XY: 0.336 AC XY: 24991AN XY: 74282 show subpopulations
GnomAD4 genome
AF:
AC:
50713
AN:
151984
Hom.:
Cov.:
32
AF XY:
AC XY:
24991
AN XY:
74282
show subpopulations
African (AFR)
AF:
AC:
16742
AN:
41432
American (AMR)
AF:
AC:
4909
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
888
AN:
3468
East Asian (EAS)
AF:
AC:
1923
AN:
5142
South Asian (SAS)
AF:
AC:
2535
AN:
4802
European-Finnish (FIN)
AF:
AC:
3377
AN:
10566
Middle Eastern (MID)
AF:
AC:
93
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19231
AN:
67978
Other (OTH)
AF:
AC:
678
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1719
3438
5157
6876
8595
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
522
1044
1566
2088
2610
<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:
1539
AN:
3478
ClinVar
Not reported inComputational 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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