11-132146480-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001352005.2(NTM):​c.366C>T​(p.His122His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00386 in 1,614,134 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0040 ( 25 hom. )

Consequence

NTM
NM_001352005.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.486
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 11-132146480-C-T is Benign according to our data. Variant chr11-132146480-C-T is described in ClinVar as [Benign]. Clinvar id is 3387950.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.486 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 25 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NTMNM_001352005.2 linkc.366C>T p.His122His synonymous_variant Exon 3 of 9 ENST00000683400.1 NP_001338934.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NTMENST00000683400.1 linkc.366C>T p.His122His synonymous_variant Exon 3 of 9 NM_001352005.2 ENSP00000507313.1 B7Z1Z5

Frequencies

GnomAD3 genomes
AF:
0.00280
AC:
426
AN:
152140
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000483
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00262
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00767
Gnomad FIN
AF:
0.00151
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.00435
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00374
AC:
938
AN:
250860
Hom.:
8
AF XY:
0.00429
AC XY:
582
AN XY:
135606
show subpopulations
Gnomad AFR exome
AF:
0.000492
Gnomad AMR exome
AF:
0.00208
Gnomad ASJ exome
AF:
0.00318
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00970
Gnomad FIN exome
AF:
0.00185
Gnomad NFE exome
AF:
0.00418
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00397
AC:
5808
AN:
1461876
Hom.:
25
Cov.:
31
AF XY:
0.00428
AC XY:
3110
AN XY:
727238
show subpopulations
Gnomad4 AFR exome
AF:
0.000657
Gnomad4 AMR exome
AF:
0.00233
Gnomad4 ASJ exome
AF:
0.00310
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0105
Gnomad4 FIN exome
AF:
0.00185
Gnomad4 NFE exome
AF:
0.00388
Gnomad4 OTH exome
AF:
0.00373
GnomAD4 genome
AF:
0.00279
AC:
425
AN:
152258
Hom.:
1
Cov.:
33
AF XY:
0.00293
AC XY:
218
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.000481
Gnomad4 AMR
AF:
0.00261
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00768
Gnomad4 FIN
AF:
0.00151
Gnomad4 NFE
AF:
0.00435
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00349
Hom.:
1
Bravo
AF:
0.00267
Asia WGS
AF:
0.00318
AC:
11
AN:
3478
EpiCase
AF:
0.00480
EpiControl
AF:
0.00528

ClinVar

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

Submissions by phenotype

not provided Benign:1
Oct 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

NTM: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.34
CADD
Benign
9.2
DANN
Benign
0.72

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: rs117450810; hg19: chr11-132016374; API