11-131466180-G-T

Position:

• chr11-131466180-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

NTM (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+95292G>T		intron_variant		ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.82+95292G>T		intron_variant			NM_001352005.2	ENSP00000507313.1

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.0455

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.0570 Hom.: 329

Bravo AF: 0.127

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs992564; hg19: chr11-131336074;