dbSNP rs2305272: 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. Variant has been reported in ClinVar as (no stars).

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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new If you want to explore the variant's impact on the transcript NM_001352005.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352005.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NTM	NM_001352005.2	MANE Select	c.527-20C>T	intron	N/A	NP_001338934.1	B7Z1Z5
NTM	NM_001352001.2		c.527-20C>T	intron	N/A	NP_001338930.1
NTM	NM_001352002.2		c.527-20C>T	intron	N/A	NP_001338931.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NTM	ENST00000683400.1	MANE Select	c.527-20C>T	intron	N/A	ENSP00000507313.1	B7Z1Z5
NTM	ENST00000425719.6	TSL:1	c.527-20C>T	intron	N/A	ENSP00000396722.2	Q9P121-4
NTM	ENST00000374786.5	TSL:1	c.527-20C>T	intron	N/A	ENSP00000363918.1	Q9P121-1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over