11-131716288-C-T

Position:

• chr11-131716288-C-T

Variant summary

Our verdict is Benign. Variant got -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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NTM	NM_001352005.2	c.83-195276C>T		intron_variant		ENST00000683400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTM	ENST00000683400.1	c.83-195276C>T		intron_variant			NM_001352005.2	A1
NTM	ENST00000374791.7	c.83-195276C>T		intron_variant		1		A1
NTM	ENST00000436745.5	c.55+55240C>T		intron_variant		3
NTM	ENST00000550167.5	c.55+55240C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.167

Alfa AF: 0.154 Hom.: 251

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs796873; hg19: chr11-131586182;