rs7481514

Variant names:

• chr11-131422069-A-G
• rs7481514
• NM_001352005.2:c.82+51181A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-131422069-A-G
• chr11-131422069-A-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+51181A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,084 control chromosomes in the GnomAD database, including 38,594 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 0.71 (38594 hom., cov: 32)
• Consequence: NTM NM_001352005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2	c.82+51181A>G		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+51181A>G		intron_variant	Intron 1 of 8		NM_001352005.2	ENSP00000507313.1
NTM	ENST00000374791.7	c.82+51181A>G		intron_variant	Intron 1 of 7	1		ENSP00000363923.3
NTM	ENST00000436745.5	c.-66+51181A>G		intron_variant	Intron 1 of 2	3		ENSP00000409221.1
NTM	ENST00000477098.1	n.260+51181A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107708 AN: 151966 Hom.: 38541 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.709 AC: 107824 AN: 152084 Hom.: 38594 Cov.: 32 AF XY: 0.711 AC XY: 52847 AN XY: 74332

African (AFR) AF: 0.781 AC: 32434 AN: 41504

American (AMR) AF: 0.713 AC: 10887 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2258 AN: 3464

East Asian (EAS) AF: 0.902 AC: 4653 AN: 5160

South Asian (SAS) AF: 0.647 AC: 3114 AN: 4814

European-Finnish (FIN) AF: 0.758 AC: 8011 AN: 10574

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44139 AN: 67982

Other (OTH) AF: 0.720 AC: 1520 AN: 2110

Alfa AF: 0.647 Hom.: 15694

Bravo AF: 0.713

Asia WGS AF: 0.757 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.075
DANN	Benign	0.20
PhyloP100		-1.5
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: rs7481514; hg19: chr11-131291963;