11-131450296-T-C

Position:

• chr11-131450296-T-C

Variant summary

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

The NM_001352005.2(NTM):​c.82+79408T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,142 control chromosomes in the GnomAD database, including 44,800 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 0.76 (44800 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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]

NTM (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+79408T>C		intron_variant		ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.82+79408T>C		intron_variant			NM_001352005.2	ENSP00000507313.1
NTM	ENST00000374791.7	c.82+79408T>C		intron_variant		1		ENSP00000363923.3
NTM	ENST00000436745.5	c.-66+79408T>C		intron_variant		3		ENSP00000409221.1
NTM	ENST00000477098.1	n.260+79408T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115782 AN: 152024 Hom.: 44772 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.762 AC: 115859 AN: 152142 Hom.: 44800 Cov.: 32 AF XY: 0.762 AC XY: 56651 AN XY: 74368

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.716

Alfa AF: 0.725 Hom.: 12593

Bravo AF: 0.765

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.042
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448363; hg19: chr11-131320190;