rs35974940

Positions:

• chr11-131375192-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001352005.2(NTM):​c.82+4304G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 152,102 control chromosomes in the GnomAD database, including 98 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 0.033 (98 hom., cov: 33)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

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=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0327 (4981/152102) while in subpopulation NFE AF= 0.0377 (2562/67994). AF 95% confidence interval is 0.0365. There are 98 homozygotes in gnomad4. There are 2353 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 98 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+4304G>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+4304G>T		intron_variant			NM_001352005.2	ENSP00000507313.1
NTM	ENST00000374791.7	c.82+4304G>T		intron_variant		1		ENSP00000363923.3
NTM	ENST00000436745.5	c.-66+4304G>T		intron_variant		3		ENSP00000409221.1
NTM	ENST00000477098.1	n.260+4304G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4979 AN: 151984 Hom.: 98 Cov.: 33

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0377

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0327 AC: 4981 AN: 152102 Hom.: 98 Cov.: 33 AF XY: 0.0316 AC XY: 2353 AN XY: 74352

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0231

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0377

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0325 Hom.: 11

Bravo AF: 0.0333

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35974940; hg19: chr11-131245087;