rs433406

chr11-131501125-A-Gchr11-131501125-A-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+130237A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,816 control chromosomes in the GnomAD database, including 21,973 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 0.52 (21973 hom., cov: 30)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970

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 (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTM	NM_001352005.2	c.82+130237A>G		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.82+130237A>G		intron_variant			NM_001352005.2	A1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79409 AN: 151698 Hom.: 21947 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.524 AC: 79491 AN: 151816 Hom.: 21973 Cov.: 30 AF XY: 0.526 AC XY: 39008 AN XY: 74170

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.490

Alfa AF: 0.472 Hom.: 3652

Bravo AF: 0.527

Asia WGS AF: 0.551 AC: 1916 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	0.20
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs433406; hg19: chr11-131371019;