rs3099797

Variant names:

• chr11-132251492-C-T
• rs3099797
• NM_001352005.2:c.526+39345C>T

Variant summary

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

The NM_001352005.2(NTM):​c.526+39345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,080 control chromosomes in the GnomAD database, including 9,711 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 0.34 (9711 hom., cov: 33)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.526+39345C>T		intron_variant	Intron 4 of 8	ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.526+39345C>T		intron_variant	Intron 4 of 8		NM_001352005.2	ENSP00000507313.1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51947 AN: 151962 Hom.: 9702 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.342 AC: 51985 AN: 152080 Hom.: 9711 Cov.: 33 AF XY: 0.343 AC XY: 25484 AN XY: 74344

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.345

Alfa AF: 0.396 Hom.: 11449

Bravo AF: 0.324

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs3099797; hg19: chr11-132121386;