rs11601906

chr11-131455352-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352005.2(NTM):c.82+84464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,394 control chromosomes in the GnomAD database, including 132 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 0.036 (132 hom., cov: 33)
  • Exomes 𝑓: 0.078 (0 hom.)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTM	NM_001352005.2	c.82+84464C>T		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.82+84464C>T		intron_variant			NM_001352005.2	A1
NTM	ENST00000374791.7	c.82+84464C>T		intron_variant		1		A1
NTM	ENST00000436745.5	c.-66+84464C>T		intron_variant		3
NTM	ENST00000477098.1	n.260+84464C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5400 AN: 152212 Hom.: 132 Cov.: 33

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0229

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0358

GnomAD4 exome AF: 0.0781 AC: 5 AN: 64 Hom.: 0 AF XY: 0.0800 AC XY: 4 AN XY: 50

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0769

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0355 AC: 5412 AN: 152330 Hom.: 132 Cov.: 33 AF XY: 0.0348 AC XY: 2594 AN XY: 74492

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0315

Gnomad4 NFE AF: 0.0458

Gnomad4 OTH AF: 0.0354

Alfa AF: 0.0389 Hom.: 46

Bravo AF: 0.0343

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.20
Dann	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11601906; hg19: chr11-131325246;