11-131785725-C-T

Variant names:

• chr11-131785725-C-T
• rs1526562
• NM_001352005.2:c.83-125839C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352005.2(NTM):​c.83-125839C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,050 control chromosomes in the GnomAD database, including 20,981 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 0.52 (20981 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.83-125839C>T		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.83-125839C>T		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1
NTM	ENST00000374791.7	c.83-125839C>T		intron_variant	Intron 1 of 7	1		ENSP00000363923.3
NTM	ENST00000550167.5	c.55+124677C>T		intron_variant	Intron 2 of 5	5		ENSP00000448104.1
NTM	ENST00000436745.5	c.55+124677C>T		intron_variant	Intron 2 of 2	3		ENSP00000409221.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78838 AN: 151932 Hom.: 20959 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.519 AC: 78917 AN: 152050 Hom.: 20981 Cov.: 32 AF XY: 0.521 AC XY: 38698 AN XY: 74326

African (AFR) AF: 0.621 AC: 25782 AN: 41488

American (AMR) AF: 0.573 AC: 8752 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2206 AN: 5166

South Asian (SAS) AF: 0.534 AC: 2571 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5221 AN: 10548

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31056 AN: 67966

Other (OTH) AF: 0.494 AC: 1040 AN: 2106

Alfa AF: 0.478 Hom.: 23329

Bravo AF: 0.529

Asia WGS AF: 0.489 AC: 1699 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	0.89
DANN	Benign	0.42
PhyloP100		0.0020
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: rs1526562; hg19: chr11-131655619;