NM_001352005.2:c.366C>T

Variant names:

• chr11-132146480-C-T
• rs117450810
• NM_001352005.2:c.366C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_001352005.2(NTM):​c.366C>T​(p.His122His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00386 in 1,614,134 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0028 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0040 (25 hom.)
• Consequence: NTM NM_001352005.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.486
• Publications: 1 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 11-132146480-C-T is Benign according to our data. Variant chr11-132146480-C-T is described in ClinVar as Benign. ClinVar VariationId is 3387950.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.486 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 25 gene

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.366C>T	p.His122His	synonymous	Exon 3 of 9	NP_001338934.1	B7Z1Z5
	NTM	NM_001352001.2		c.366C>T	p.His122His	synonymous	Exon 3 of 10	NP_001338930.1
	NTM	NM_001352002.2		c.366C>T	p.His122His	synonymous	Exon 2 of 9	NP_001338931.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	ENST00000683400.1	MANE Select	c.366C>T	p.His122His	synonymous	Exon 3 of 9	ENSP00000507313.1	B7Z1Z5
	NTM	ENST00000425719.6	TSL:1	c.366C>T	p.His122His	synonymous	Exon 2 of 8	ENSP00000396722.2	Q9P121-4
	NTM	ENST00000374786.5	TSL:1	c.366C>T	p.His122His	synonymous	Exon 2 of 7	ENSP00000363918.1	Q9P121-1

Frequencies

GnomAD3 genomes AF: 0.00280 AC: 426 AN: 152140 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000483

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00262

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00435

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00374 AC: 938 AN: 250860 AF XY: 0.00429

Gnomad AFR exome AF: 0.000492

Gnomad AMR exome AF: 0.00208

Gnomad ASJ exome AF: 0.00318

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00185

Gnomad NFE exome AF: 0.00418

Gnomad OTH exome AF: 0.00261

GnomAD4 exome AF: 0.00397 AC: 5808 AN: 1461876 Hom.: 25 Cov.: 31 AF XY: 0.00428 AC XY: 3110 AN XY: 727238

African (AFR) AF: 0.000657 AC: 22 AN: 33480

American (AMR) AF: 0.00233 AC: 104 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00310 AC: 81 AN: 26136

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39698

South Asian (SAS) AF: 0.0105 AC: 909 AN: 86256

European-Finnish (FIN) AF: 0.00185 AC: 99 AN: 53416

Middle Eastern (MID) AF: 0.00936 AC: 54 AN: 5768

European-Non Finnish (NFE) AF: 0.00388 AC: 4313 AN: 1112002

Other (OTH) AF: 0.00373 AC: 225 AN: 60396

GnomAD4 genome AF: 0.00279 AC: 425 AN: 152258 Hom.: 1 Cov.: 33 AF XY: 0.00293 AC XY: 218 AN XY: 74448

African (AFR) AF: 0.000481 AC: 20 AN: 41544

American (AMR) AF: 0.00261 AC: 40 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00768 AC: 37 AN: 4820

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10608

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00435 AC: 296 AN: 68022

Other (OTH) AF: 0.00284 AC: 6 AN: 2114

Alfa AF: 0.00349 Hom.: 1

Bravo AF: 0.00267

Asia WGS AF: 0.00318 AC: 11 AN: 3478

EpiCase AF: 0.00480

EpiControl AF: 0.00528

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	9.2
DANN	Benign	0.72
PhyloP100		0.49
PromoterAI		-0.017	Neutral
Mutation Taster		=95/5	polymorphism

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: rs117450810; hg19: chr11-132016374;