11-132030663-T-G

Variant names:

• chr11-132030663-T-G
• rs6590611
• NM_001352005.2:c.168-115619T>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.168-115619T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,034 control chromosomes in the GnomAD database, including 33,152 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 0.66 (33152 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352005.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	NM_001352005.2	MANE Select	c.168-115619T>G		intron	N/A	NP_001338934.1
	NTM	NM_001352001.2		c.168-115619T>G		intron	N/A	NP_001338930.1
	NTM	NM_001352002.2		c.168-115619T>G		intron	N/A	NP_001338931.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	ENST00000683400.1	MANE Select	c.168-115619T>G		intron	N/A	ENSP00000507313.1
	NTM	ENST00000425719.6	TSL:1	c.168-115619T>G		intron	N/A	ENSP00000396722.2
	NTM	ENST00000374786.5	TSL:1	c.168-115619T>G		intron	N/A	ENSP00000363918.1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99874 AN: 151918 Hom.: 33146 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.657 AC: 99918 AN: 152034 Hom.: 33152 Cov.: 32 AF XY: 0.659 AC XY: 48966 AN XY: 74318

African (AFR) AF: 0.601 AC: 24916 AN: 41466

American (AMR) AF: 0.587 AC: 8964 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2322 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4262 AN: 5152

South Asian (SAS) AF: 0.709 AC: 3401 AN: 4798

European-Finnish (FIN) AF: 0.714 AC: 7542 AN: 10564

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46339 AN: 68000

Other (OTH) AF: 0.663 AC: 1399 AN: 2110

Alfa AF: 0.662 Hom.: 16128

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.083
DANN	Benign	0.53
PhyloP100		-1.4
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: rs6590611; hg19: chr11-131900557;