chr11-131557666-C-T

Variant names:

• chr11-131557666-C-T
• rs11222692
• NM_001352005.2:c.82+186778C>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.82+186778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0617 in 149,920 control chromosomes in the GnomAD database, including 349 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 0.062 (349 hom., cov: 31)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 2 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]

ENSG00000285980 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+186778C>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.82+186778C>T		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1

Frequencies

GnomAD3 genomes AF: 0.0617 AC: 9240 AN: 149810 Hom.: 351 Cov.: 31

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0651

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0838

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0610

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

GnomAD4 genome AF: 0.0617 AC: 9244 AN: 149920 Hom.: 349 Cov.: 31 AF XY: 0.0617 AC XY: 4505 AN XY: 73010

African (AFR) AF: 0.0151 AC: 615 AN: 40658

American (AMR) AF: 0.0691 AC: 1032 AN: 14936

Ashkenazi Jewish (ASJ) AF: 0.0612 AC: 212 AN: 3464

East Asian (EAS) AF: 0.190 AC: 957 AN: 5042

South Asian (SAS) AF: 0.0830 AC: 393 AN: 4736

European-Finnish (FIN) AF: 0.0605 AC: 605 AN: 9998

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0771 AC: 5228 AN: 67800

Other (OTH) AF: 0.0608 AC: 127 AN: 2088

Alfa AF: 0.0705 Hom.: 521

Bravo AF: 0.0583

Asia WGS AF: 0.123 AC: 428 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	1.4
DANN	Benign	0.65
PhyloP100		-0.72
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: rs11222692; hg19: chr11-131427560;