11-132140223-T-C

Variant names:

• chr11-132140223-T-C
• rs4468361
• NM_001352005.2:c.168-6059T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352005.2(NTM):​c.168-6059T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,870 control chromosomes in the GnomAD database, including 32,187 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 0.65 (32187 hom., cov: 31)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352005.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	NM_001352005.2	MANE Select	c.168-6059T>C		intron	N/A	NP_001338934.1
	NTM	NM_001352001.2		c.168-6059T>C		intron	N/A	NP_001338930.1
	NTM	NM_001352002.2		c.168-6059T>C		intron	N/A	NP_001338931.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	ENST00000683400.1	MANE Select	c.168-6059T>C		intron	N/A	ENSP00000507313.1
	NTM	ENST00000425719.6	TSL:1	c.168-6059T>C		intron	N/A	ENSP00000396722.2
	NTM	ENST00000374786.5	TSL:1	c.168-6059T>C		intron	N/A	ENSP00000363918.1

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98248 AN: 151752 Hom.: 32148 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.655

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.648 AC: 98345 AN: 151870 Hom.: 32187 Cov.: 31 AF XY: 0.642 AC XY: 47658 AN XY: 74212

African (AFR) AF: 0.652 AC: 26950 AN: 41358

American (AMR) AF: 0.628 AC: 9589 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1896 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2385 AN: 5116

South Asian (SAS) AF: 0.567 AC: 2728 AN: 4812

European-Finnish (FIN) AF: 0.645 AC: 6810 AN: 10556

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45827 AN: 67976

Other (OTH) AF: 0.653 AC: 1377 AN: 2110

Alfa AF: 0.660 Hom.: 106976

Bravo AF: 0.652

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.039
DANN	Benign	0.36
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4468361; hg19: chr11-132010117;