rs1543121

Variant names:

• chr11-131528640-G-T
• rs1543121
• NM_001352005.2:c.82+157752G>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.82+157752G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,212 control chromosomes in the GnomAD database, including 572 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 0.081 (572 hom., cov: 33)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 3 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+157752G>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.82+157752G>T		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12374 AN: 152094 Hom.: 573 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0813 AC: 12382 AN: 152212 Hom.: 572 Cov.: 33 AF XY: 0.0810 AC XY: 6030 AN XY: 74416

African (AFR) AF: 0.124 AC: 5132 AN: 41526

American (AMR) AF: 0.0976 AC: 1491 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3468

East Asian (EAS) AF: 0.0230 AC: 119 AN: 5178

South Asian (SAS) AF: 0.0891 AC: 429 AN: 4816

European-Finnish (FIN) AF: 0.0645 AC: 683 AN: 10594

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0581 AC: 3955 AN: 68026

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0690 Hom.: 667

Bravo AF: 0.0872

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.058
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: rs1543121; hg19: chr11-131398534;