chr11-131945450-T-G

Variant names:

• chr11-131945450-T-G
• rs544166
• NM_001352005.2:c.167+33802T>G

Variant summary

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

The NM_001352005.2(NTM):​c.167+33802T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,984 control chromosomes in the GnomAD database, including 8,882 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 0.33 (8882 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.167+33802T>G		intron_variant	Intron 2 of 8	ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.167+33802T>G		intron_variant	Intron 2 of 8		NM_001352005.2	ENSP00000507313.1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50651 AN: 151866 Hom.: 8873 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.334 AC: 50713 AN: 151984 Hom.: 8882 Cov.: 32 AF XY: 0.336 AC XY: 24991 AN XY: 74282

African (AFR) AF: 0.404 AC: 16742 AN: 41432

American (AMR) AF: 0.321 AC: 4909 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1923 AN: 5142

South Asian (SAS) AF: 0.528 AC: 2535 AN: 4802

European-Finnish (FIN) AF: 0.320 AC: 3377 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19231 AN: 67978

Other (OTH) AF: 0.320 AC: 678 AN: 2116

Alfa AF: 0.299 Hom.: 11815

Bravo AF: 0.336

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.81
DANN	Benign	0.72
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs544166; hg19: chr11-131815344;