rs4456263

Positions:

• chr11-131783404-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.83-128160C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,910 control chromosomes in the GnomAD database, including 18,804 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 0.49 (18804 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTM	NM_001352005.2	c.83-128160C>T		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.83-128160C>T		intron_variant			NM_001352005.2	A1
NTM	ENST00000374791.7	c.83-128160C>T		intron_variant		1		A1
NTM	ENST00000436745.5	c.55+122356C>T		intron_variant		3
NTM	ENST00000550167.5	c.55+122356C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74855 AN: 151790 Hom.: 18782 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.493 AC: 74935 AN: 151910 Hom.: 18804 Cov.: 32 AF XY: 0.495 AC XY: 36723 AN XY: 74236

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.461

Alfa AF: 0.454 Hom.: 21049

Bravo AF: 0.503

Asia WGS AF: 0.469 AC: 1628 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456263; hg19: chr11-131653298;