11-131466180-G-T

Variant names:

• chr11-131466180-G-T
• rs992564
• NM_001352005.2:c.82+95292G>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+95292G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,200 control chromosomes in the GnomAD database, including 1,827 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 0.11 (1827 hom., cov: 33)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.514 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.82+95292G>T		intron	N/A	NP_001338934.1	B7Z1Z5
	NTM	NM_001352001.2		c.82+95292G>T		intron	N/A	NP_001338930.1
	NTM	NM_001352003.2		c.82+95292G>T		intron	N/A	NP_001338932.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTM	ENST00000683400.1	MANE Select	c.82+95292G>T		intron	N/A	ENSP00000507313.1	B7Z1Z5
	NTM	ENST00000374791.7	TSL:1	c.82+95292G>T		intron	N/A	ENSP00000363923.3	Q9P121-2
	NTM	ENST00000550167.5	TSL:5	c.-66+10713G>T		intron	N/A	ENSP00000448104.1	F8VTR5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16291 AN: 152082 Hom.: 1814 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0455

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.107 AC: 16322 AN: 152200 Hom.: 1827 Cov.: 33 AF XY: 0.114 AC XY: 8480 AN XY: 74390

African (AFR) AF: 0.112 AC: 4653 AN: 41518

American (AMR) AF: 0.252 AC: 3853 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2737 AN: 5162

South Asian (SAS) AF: 0.136 AC: 653 AN: 4816

European-Finnish (FIN) AF: 0.0943 AC: 1001 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3094 AN: 68020

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0736 Hom.: 2103

Bravo AF: 0.127

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.58
PhyloP100		-0.17
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: rs992564; hg19: chr11-131336074;