11-131971675-A-G

Variant names:

• chr11-131971675-A-G
• rs3345
• NM_001352005.2:c.167+60027A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352005.2(NTM):​c.167+60027A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,494 control chromosomes in the GnomAD database, including 14,966 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 0.43 (14966 hom., cov: 29)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.167+60027A>G		intron_variant	Intron 2 of 8	ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.167+60027A>G		intron_variant	Intron 2 of 8		NM_001352005.2	ENSP00000507313.1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65563 AN: 151376 Hom.: 14914 Cov.: 29

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.434 AC: 65673 AN: 151494 Hom.: 14966 Cov.: 29 AF XY: 0.440 AC XY: 32557 AN XY: 73992

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.456

Alfa AF: 0.375 Hom.: 2300

Bravo AF: 0.447

Asia WGS AF: 0.638 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs3345; hg19: chr11-131841569;