NM_001352005.2:c.82+79408T>C

Variant names:

• chr11-131450296-T-C
• rs1448363
• NM_001352005.2:c.82+79408T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352005.2(NTM):​c.82+79408T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,142 control chromosomes in the GnomAD database, including 44,800 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 0.76 (44800 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+79408T>C		intron_variant	Intron 1 of 8	ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.82+79408T>C		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1
NTM	ENST00000374791.7	c.82+79408T>C		intron_variant	Intron 1 of 7	1		ENSP00000363923.3
NTM	ENST00000436745.5	c.-66+79408T>C		intron_variant	Intron 1 of 2	3		ENSP00000409221.1
NTM	ENST00000477098.1	n.260+79408T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115782 AN: 152024 Hom.: 44772 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.762 AC: 115859 AN: 152142 Hom.: 44800 Cov.: 32 AF XY: 0.762 AC XY: 56651 AN XY: 74368

African (AFR) AF: 0.867 AC: 36006 AN: 41512

American (AMR) AF: 0.746 AC: 11394 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2021 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5015 AN: 5166

South Asian (SAS) AF: 0.582 AC: 2802 AN: 4816

European-Finnish (FIN) AF: 0.791 AC: 8375 AN: 10582

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47931 AN: 67996

Other (OTH) AF: 0.716 AC: 1513 AN: 2112

Alfa AF: 0.727 Hom.: 15946

Bravo AF: 0.765

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.042
DANN	Benign	0.32
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1448363; hg19: chr11-131320190;