rs576825

chr11-131824982-A-C

Variant summary

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

The NM_001352005.2(NTM):c.83-86582A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,072 control chromosomes in the GnomAD database, including 10,607 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 0.37 (10607 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTM	NM_001352005.2	c.83-86582A>C		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.83-86582A>C		intron_variant			NM_001352005.2	A1
NTM	ENST00000374791.7	c.83-86582A>C		intron_variant		1		A1
NTM	ENST00000436745.5	c.56-86582A>C		intron_variant		3
NTM	ENST00000550167.5	c.56-86582A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55563 AN: 151954 Hom.: 10598 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.366 AC: 55603 AN: 152072 Hom.: 10607 Cov.: 32 AF XY: 0.367 AC XY: 27275 AN XY: 74332

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.359

Alfa AF: 0.334 Hom.: 17809

Bravo AF: 0.365

Asia WGS AF: 0.328 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs576825; hg19: chr11-131694876;