dbSNP rs1065663: NUBP2:c.*308G>A (chr16-1789022-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012225.4(NUBP2):c.*308G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 347,590 control chromosomes in the GnomAD database, including 114,771 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 0.84 ( 53928 hom., cov: 35)

Exomes 𝑓: 0.79 ( 60843 hom. )

Consequence

NUBP2
NM_012225.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81

Publications

20 publications found

Variant links:

Genes affected

NUBP2 (HGNC:8042): (NUBP iron-sulfur cluster assembly factor 2, cytosolic) This gene encodes an adenosine triphosphate (ATP) and metal-binding protein that is required for the assembly of cyotosolic iron-sulfur proteins. The encoded protein functions in a heterotetramer with nucleotide-binding protein 1 (NUBP1). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2013]

NUBP2 links:

SPSB3 (HGNC:30629): (splA/ryanodine receptor domain and SOCS box containing 3) Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be located in cytosol. Predicted to be part of SCF ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

SPSB3 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUBP2	NM_012225.4 link	c.*308G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000262302.14	NP_036357.1	Q9Y5Y2B7Z6P0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUBP2	ENST00000262302.14 link	c.*308G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_012225.4	ENSP00000262302.9		Q9Y5Y2

Frequencies

GnomAD3 genomes

AF:

0.838

AC:

127518

AN:

152180

Hom.:

53869

Cov.:

show subpopulations

Gnomad AFR

AF:

0.936

Gnomad AMI

AF:

0.887

Gnomad AMR

AF:

0.818

Gnomad ASJ

AF:

0.849

Gnomad EAS

AF:

0.721

Gnomad SAS

AF:

0.764

Gnomad FIN

AF:

0.708

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.815

Gnomad OTH

AF:

0.850

GnomAD4 exome

AF:

0.786

AC:

153528

AN:

195292

Hom.:

60843

Cov.:

AF XY:

0.782

AC XY:

78848

AN XY:

100820

show subpopulations

African (AFR)

AF:

0.935

AC:

5411

AN:

5786

American (AMR)

AF:

0.785

AC:

4822

AN:

6144

Ashkenazi Jewish (ASJ)

AF:

0.839

AC:

5692

AN:

6786

East Asian (EAS)

AF:

0.650

AC:

8445

AN:

12984

South Asian (SAS)

AF:

0.719

AC:

11347

AN:

15784

European-Finnish (FIN)

AF:

0.718

AC:

8758

AN:

12200

Middle Eastern (MID)

AF:

0.850

AC:

840

AN:

988

European-Non Finnish (NFE)

AF:

0.804

AC:

98323

AN:

122284

Other (OTH)

AF:

0.802

AC:

9890

AN:

12336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1478

2956

4435

5913

7391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.838

AC:

127636

AN:

152298

Hom.:

53928

Cov.:

AF XY:

0.829

AC XY:

61740

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.937

AC:

38953

AN:

41592

American (AMR)

AF:

0.818

AC:

12521

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.849

AC:

2949

AN:

3472

East Asian (EAS)

AF:

0.721

AC:

3725

AN:

5170

South Asian (SAS)

AF:

0.764

AC:

3693

AN:

4832

European-Finnish (FIN)

AF:

0.708

AC:

7512

AN:

10606

Middle Eastern (MID)

AF:

0.864

AC:

254

AN:

294

European-Non Finnish (NFE)

AF:

0.815

AC:

55424

AN:

68004

Other (OTH)

AF:

0.850

AC:

1796

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1082

2164

3245

4327

5409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

880

1760

2640

3520

4400

<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:

0.829

Hom.:

87778

Bravo

AF:

0.854

Asia WGS

AF:

0.737

AC:

2564

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.096

(source)

DANN

Benign

0.59

PhyloP100

-1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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