rs12421680

Positions:

• chr11-131481074-G-A
• chr11-131481074-G-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+110186G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,864 control chromosomes in the GnomAD database, including 16,732 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 0.45 (16732 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTM	NM_001352005.2	c.82+110186G>A		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.82+110186G>A		intron_variant			NM_001352005.2	A1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68411 AN: 151746 Hom.: 16697 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.451 AC: 68510 AN: 151864 Hom.: 16732 Cov.: 32 AF XY: 0.456 AC XY: 33803 AN XY: 74200

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.419

Alfa AF: 0.365 Hom.: 21684

Bravo AF: 0.471

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12421680; hg19: chr11-131350968;