dbSNP rs10507140: NUP37:c.541-1479G>C (chr12-102078982-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024057.4(NUP37):c.541-1479G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 207,800 control chromosomes in the GnomAD database, including 542 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 0.035 ( 386 hom., cov: 32)

Exomes 𝑓: 0.038 ( 156 hom. )

Consequence

NUP37
NM_024057.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.217

Publications

0 publications found

Variant links:

Genes affected

NUP37 (HGNC:29929): (nucleoporin 37) Nuclear pore complexes (NPCs) are used for transporting macromolecules between the cytoplasm and the nucleus. NPCs consist of multiple copies of 30 distinct proteins (nucleoporins), which assemble into biochemically-separable subcomplexes. The protein encoded by this gene is part of a subcomplex (Nup107-160) that is required for proper NPC function as well as for normal kinetochore-microtubule interaction and mitosis. [provided by RefSeq, Dec 2015]

NUP37 Gene-Disease associations (from GenCC):

familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

NUP37 links:

Genome browser will be placed here

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP37	NM_024057.4 link	c.541-1479G>C		intron_variant	Intron 6 of 9	ENST00000552283.6	NP_076962.2	Q8NFH4
NUP37	XM_047429530.1 link	c.*229G>C		downstream_gene_variant			XP_047285486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP37	ENST00000552283.6 link	c.541-1479G>C		intron_variant	Intron 6 of 9	5	NM_024057.4	ENSP00000448054.1		Q8NFH4

Frequencies

GnomAD3 genomes

AF:

0.0354

AC:

5384

AN:

152104

Hom.:

382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00640

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0972

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.0597

Gnomad FIN

AF:

0.0791

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0129

Gnomad OTH

AF:

0.0420

GnomAD4 exome

AF:

0.0381

AC:

2116

AN:

55578

Hom.:

156

AF XY:

0.0393

AC XY:

1171

AN XY:

29780

show subpopulations

African (AFR)

AF:

0.00625

AC:

AN:

1440

American (AMR)

AF:

0.108

AC:

263

AN:

2438

Ashkenazi Jewish (ASJ)

AF:

0.00537

AC:

AN:

1304

East Asian (EAS)

AF:

0.298

AC:

745

AN:

2502

South Asian (SAS)

AF:

0.0448

AC:

364

AN:

8120

European-Finnish (FIN)

AF:

0.0638

AC:

166

AN:

2600

Middle Eastern (MID)

AF:

0.00303

AC:

AN:

1648

European-Non Finnish (NFE)

AF:

0.0133

AC:

432

AN:

32388

Other (OTH)

AF:

0.0398

AC:

125

AN:

3138

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

188

281

375

469

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<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:

0.0354

AC:

5396

AN:

152222

Hom.:

386

Cov.:

AF XY:

0.0407

AC XY:

3028

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.00638

AC:

265

AN:

41544

American (AMR)

AF:

0.0980

AC:

1499

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.295

AC:

1529

AN:

5182

South Asian (SAS)

AF:

0.0600

AC:

289

AN:

4820

European-Finnish (FIN)

AF:

0.0791

AC:

837

AN:

10586

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0129

AC:

879

AN:

68006

Other (OTH)

AF:

0.0421

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

226

453

679

906

1132

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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:

0.0107

Hom.:

Bravo

AF:

0.0368

Asia WGS

AF:

0.197

AC:

681

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.98

(source)

DANN

Benign

0.34

PhyloP100

-0.22

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