11-131926818-C-T

Variant names:

• chr11-131926818-C-T
• rs497747
• NM_001352005.2:c.167+15170C>T

Variant summary

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

The NM_001352005.2(NTM):​c.167+15170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,000 control chromosomes in the GnomAD database, including 24,578 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 0.56 (24578 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	NM_001352005.2	MANE Select	c.167+15170C>T		intron	N/A	NP_001338934.1	B7Z1Z5
	NTM	NM_001352001.2		c.167+15170C>T		intron	N/A	NP_001338930.1
	NTM	NM_001352002.2		c.167+15170C>T		intron	N/A	NP_001338931.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	ENST00000683400.1	MANE Select	c.167+15170C>T		intron	N/A	ENSP00000507313.1	B7Z1Z5
	NTM	ENST00000425719.6	TSL:1	c.167+15170C>T		intron	N/A	ENSP00000396722.2	Q9P121-4
	NTM	ENST00000374786.5	TSL:1	c.167+15170C>T		intron	N/A	ENSP00000363918.1	Q9P121-1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85357 AN: 151882 Hom.: 24542 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.562 AC: 85446 AN: 152000 Hom.: 24578 Cov.: 32 AF XY: 0.569 AC XY: 42303 AN XY: 74286

African (AFR) AF: 0.560 AC: 23232 AN: 41464

American (AMR) AF: 0.535 AC: 8165 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3466

East Asian (EAS) AF: 0.930 AC: 4797 AN: 5160

South Asian (SAS) AF: 0.569 AC: 2734 AN: 4808

European-Finnish (FIN) AF: 0.670 AC: 7081 AN: 10568

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36226 AN: 67950

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.537 Hom.: 16836

Bravo AF: 0.558

Asia WGS AF: 0.743 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.025
DANN	Benign	0.60
PhyloP100		-1.0
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: rs497747; hg19: chr11-131796712;