chr11-131522794-T-A

Variant names:

• chr11-131522794-T-A
• rs411280
• NM_001352005.2:c.82+151906T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001352005.2(NTM):​c.82+151906T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,066 control chromosomes in the GnomAD database, including 42,375 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 0.74 (42375 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38
• Publications: 4 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]

ENSG00000237654 (HGNC:40821):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+151906T>A		intron_variant	Intron 1 of 8	ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1	c.82+151906T>A		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112474 AN: 151948 Hom.: 42315 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.740 AC: 112590 AN: 152066 Hom.: 42375 Cov.: 32 AF XY: 0.746 AC XY: 55428 AN XY: 74326

African (AFR) AF: 0.834 AC: 34590 AN: 41476

American (AMR) AF: 0.797 AC: 12188 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3468

East Asian (EAS) AF: 0.991 AC: 5130 AN: 5176

South Asian (SAS) AF: 0.722 AC: 3478 AN: 4820

European-Finnish (FIN) AF: 0.712 AC: 7521 AN: 10564

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45137 AN: 67966

Other (OTH) AF: 0.737 AC: 1554 AN: 2108

Alfa AF: 0.588 Hom.: 1623

Bravo AF: 0.754

Asia WGS AF: 0.853 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		2.4
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: rs411280; hg19: chr11-131392688;