Genetic Variant NTM:c.527-20C>T (chr11-132307669-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001352005.2(NTM):c.527-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,613,026 control chromosomes in the GnomAD database, including 27,045 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 0.16 ( 2260 hom., cov: 33)

Exomes 𝑓: 0.18 ( 24785 hom. )

Consequence

NTM
NM_001352005.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281

Publications

10 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTM	NM_001352005.2 link	c.527-20C>T		intron_variant	Intron 4 of 8	ENST00000683400.1	NP_001338934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTM	ENST00000683400.1 link	c.527-20C>T		intron_variant	Intron 4 of 8		NM_001352005.2	ENSP00000507313.1		B7Z1Z5

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23711

AN:

152080

Hom.:

2263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0608

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.183

GnomAD2 exomes

AF:

0.193

AC:

48381

AN:

250434

AF XY:

0.191

show subpopulations

Gnomad AFR exome

AF:

0.0578

Gnomad AMR exome

AF:

0.307

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.352

Gnomad FIN exome

AF:

0.129

Gnomad NFE exome

AF:

0.174

Gnomad OTH exome

AF:

0.193

GnomAD4 exome

AF:

0.178

AC:

259874

AN:

1460828

Hom.:

24785

Cov.:

AF XY:

0.178

AC XY:

129546

AN XY:

726690

show subpopulations

African (AFR)

AF:

0.0567

AC:

1896

AN:

33458

American (AMR)

AF:

0.298

AC:

13307

AN:

44628

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

4402

AN:

26110

East Asian (EAS)

AF:

0.313

AC:

12431

AN:

39674

South Asian (SAS)

AF:

0.169

AC:

14567

AN:

86166

European-Finnish (FIN)

AF:

0.129

AC:

6903

AN:

53404

Middle Eastern (MID)

AF:

0.184

AC:

1058

AN:

5764

European-Non Finnish (NFE)

AF:

0.175

AC:

194313

AN:

1111272

Other (OTH)

AF:

0.182

AC:

10997

AN:

60352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

9562

19124

28686

38248

47810

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6986

13972

20958

27944

34930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.156

AC:

23710

AN:

152198

Hom.:

2260

Cov.:

AF XY:

0.159

AC XY:

11859

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0607

AC:

2519

AN:

41522

American (AMR)

AF:

0.263

AC:

4018

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

591

AN:

3472

East Asian (EAS)

AF:

0.348

AC:

1796

AN:

5164

South Asian (SAS)

AF:

0.183

AC:

884

AN:

4826

European-Finnish (FIN)

AF:

0.117

AC:

1242

AN:

10600

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.178

AC:

12139

AN:

68006

Other (OTH)

AF:

0.186

AC:

393

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1002

2004

3006

4008

5010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.181

Hom.:

3595

Bravo

AF:

0.163

Asia WGS

AF:

0.283

AC:

983

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.44

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over