rs789550

chr11-131719532-C-A

Variant summary

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

The NM_001352005.2(NTM):c.83-192032C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,120 control chromosomes in the GnomAD database, including 1,816 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 0.15 (1816 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTM	NM_001352005.2	c.83-192032C>A		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.83-192032C>A		intron_variant			NM_001352005.2	A1
NTM	ENST00000374791.7	c.83-192032C>A		intron_variant		1		A1
NTM	ENST00000436745.5	c.55+58484C>A		intron_variant		3
NTM	ENST00000550167.5	c.55+58484C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22443 AN: 152002 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.148 AC: 22455 AN: 152120 Hom.: 1816 Cov.: 32 AF XY: 0.147 AC XY: 10947 AN XY: 74352

Gnomad4 AFR AF: 0.0921

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.163

Alfa AF: 0.149 Hom.: 202

Bravo AF: 0.146

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.079
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs789550; hg19: chr11-131589426;