rs2044727

Variant names:

• chr11-132269097-C-A
• rs2044727
• NM_001352005.2:c.527-38592C>A

Variant summary

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

The NM_001352005.2(NTM):​c.527-38592C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,996 control chromosomes in the GnomAD database, including 7,301 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 0.30 (7301 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 4 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	NM_001352005.2	MANE Select	c.527-38592C>A		intron	N/A	NP_001338934.1	B7Z1Z5
	NTM	NM_001352001.2		c.527-38592C>A		intron	N/A	NP_001338930.1
	NTM	NM_001352002.2		c.527-38592C>A		intron	N/A	NP_001338931.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	ENST00000683400.1	MANE Select	c.527-38592C>A		intron	N/A	ENSP00000507313.1	B7Z1Z5
	NTM	ENST00000425719.6	TSL:1	c.527-38592C>A		intron	N/A	ENSP00000396722.2	Q9P121-4
	NTM	ENST00000374786.5	TSL:1	c.527-38592C>A		intron	N/A	ENSP00000363918.1	Q9P121-1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46118 AN: 151878 Hom.: 7286 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.304 AC: 46171 AN: 151996 Hom.: 7301 Cov.: 32 AF XY: 0.298 AC XY: 22134 AN XY: 74286

African (AFR) AF: 0.366 AC: 15160 AN: 41438

American (AMR) AF: 0.307 AC: 4681 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1106 AN: 5146

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4814

European-Finnish (FIN) AF: 0.219 AC: 2310 AN: 10566

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19990 AN: 67986

Other (OTH) AF: 0.321 AC: 677 AN: 2110

Alfa AF: 0.291 Hom.: 3986

Bravo AF: 0.316

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.3
DANN	Benign	0.61
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: rs2044727; hg19: chr11-132138991;