dbSNP rs3214915: NUP85:c.1767+54_1767+55delTA (chr17-75234841-TTA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024844.5(NUP85):c.1767+54_1767+55delTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,603,254 control chromosomes in the GnomAD database, including 2,189 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.066 ( 907 hom., cov: 32)

Exomes 𝑓: 0.015 ( 1282 hom. )

Consequence

NUP85
NM_024844.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.113

Publications

5 publications found

Variant links:

Genes affected

NUP85 (HGNC:8734): (nucleoporin 85) This gene encodes a protein component of the Nup107-160 subunit of the nuclear pore complex. Nuclear pore complexes are embedded in the nuclear envelope and promote bidirectional transport of macromolecules between the cytoplasm and nucleus. The encoded protein can also bind to the C-terminus of chemokine (C-C motif) receptor 2 (CCR2) and promote chemotaxis of monocytes, thereby participating in the inflammatory response. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

NUP85 Gene-Disease associations (from GenCC):

nephrotic syndrome, type 17
Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Tourette syndrome
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

NUP85 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024844.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NUP85	NM_024844.5	MANE Select	c.1767+54_1767+55delTA	intron	N/A	NP_079120.1	Q9BW27-1
NUP85	NM_001330472.2		c.1632+54_1632+55delTA	intron	N/A	NP_001317401.1	J3KT10
NUP85	NM_001303276.2		c.1629+54_1629+55delTA	intron	N/A	NP_001290205.1	Q9BW27-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NUP85	ENST00000245544.9	TSL:1 MANE Select	c.1767+54_1767+55delTA	intron	N/A	ENSP00000245544.4	Q9BW27-1
NUP85	ENST00000968072.1		c.1821+54_1821+55delTA	intron	N/A	ENSP00000638131.1
NUP85	ENST00000898366.1		c.1767+54_1767+55delTA	intron	N/A	ENSP00000568425.1

Frequencies

GnomAD3 genomes

AF:

0.0662

AC:

10074

AN:

152064

Hom.:

901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0646

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.0758

Gnomad SAS

AF:

0.0833

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.00166

Gnomad OTH

AF:

0.0623

GnomAD2 exomes

AF:

0.0362

AC:

9057

AN:

250348

AF XY:

0.0336

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.0488

Gnomad ASJ exome

AF:

0.00566

Gnomad EAS exome

AF:

0.0718

Gnomad FIN exome

AF:

0.0000478

Gnomad NFE exome

AF:

0.00183

Gnomad OTH exome

AF:

0.0193

GnomAD4 exome

AF:

0.0147

AC:

21283

AN:

1451072

Hom.:

1282

AF XY:

0.0157

AC XY:

11368

AN XY:

722612

show subpopulations

African (AFR)

AF:

0.206

AC:

6860

AN:

33302

American (AMR)

AF:

0.0508

AC:

2271

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.00529

AC:

138

AN:

26078

East Asian (EAS)

AF:

0.0611

AC:

2422

AN:

39664

South Asian (SAS)

AF:

0.0764

AC:

6572

AN:

86060

European-Finnish (FIN)

AF:

0.0000191

AC:

AN:

52478

Middle Eastern (MID)

AF:

0.0268

AC:

154

AN:

5754

European-Non Finnish (NFE)

AF:

0.00116

AC:

1276

AN:

1102978

Other (OTH)

AF:

0.0265

AC:

1589

AN:

60054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1197

2393

3590

4786

5983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

380

760

1140

1520

1900

<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:

0.0663

AC:

10092

AN:

152182

Hom.:

907

Cov.:

AF XY:

0.0666

AC XY:

4957

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.194

AC:

8045

AN:

41470

American (AMR)

AF:

0.0644

AC:

985

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00404

AC:

AN:

3466

East Asian (EAS)

AF:

0.0760

AC:

394

AN:

5184

South Asian (SAS)

AF:

0.0826

AC:

399

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00166

AC:

113

AN:

68018

Other (OTH)

AF:

0.0617

AC:

130

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

417

833

1250

1666

2083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0266

Hom.:

Bravo

AF:

0.0744

Asia WGS

AF:

0.0980

AC:

342

AN:

3478

EpiCase

AF:

0.00251

EpiControl

AF:

0.00196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.11

Mutation Taster

=164/36

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over