NM_001352005.2:c.83-195276C>T

Variant names:

• chr11-131716288-C-T
• rs796873
• NM_001352005.2:c.83-195276C>T

Variant summary

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

The NM_001352005.2(NTM):​c.83-195276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,046 control chromosomes in the GnomAD database, including 2,083 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 0.16 (2083 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.83-195276C>T		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.83-195276C>T		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1
NTM	ENST00000374791.7	c.83-195276C>T		intron_variant	Intron 1 of 7	1		ENSP00000363923.3
NTM	ENST00000550167.5	c.55+55240C>T		intron_variant	Intron 2 of 5	5		ENSP00000448104.1
NTM	ENST00000436745.5	c.55+55240C>T		intron_variant	Intron 2 of 2	3		ENSP00000409221.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24547 AN: 151928 Hom.: 2082 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.161 AC: 24548 AN: 152046 Hom.: 2083 Cov.: 32 AF XY: 0.161 AC XY: 11940 AN XY: 74324

African (AFR) AF: 0.142 AC: 5899 AN: 41468

American (AMR) AF: 0.137 AC: 2100 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3462

East Asian (EAS) AF: 0.202 AC: 1040 AN: 5160

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4810

European-Finnish (FIN) AF: 0.132 AC: 1398 AN: 10572

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11626 AN: 67978

Other (OTH) AF: 0.167 AC: 353 AN: 2114

Alfa AF: 0.155 Hom.: 261

Bravo AF: 0.160

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs796873; hg19: chr11-131586182;