dbSNP rs1065212: NOP16:p.Glu183Gly (chr5-176384132-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000618911.4(NOP16):c.548A>G(p.Glu183Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 1,611,914 control chromosomes in the GnomAD database, including 7,392 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1074 hom., cov: 32)

Exomes 𝑓: 0.088 ( 6318 hom. )

Consequence

NOP16
ENST00000618911.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.502

Publications

18 publications found

Variant links:

Genes affected

NOP16 (HGNC:26934): (NOP16 nucleolar protein) This gene encodes a protein that is localized to the nucleolus. Expression of this gene is induced by estrogens and Myc protein and is a marker of poor patient survival in breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

NOP16 links:

ARL10 (HGNC:22042): (ADP ribosylation factor like GTPase 10) Predicted to enable GTP binding activity and GTPase activity. [provided by Alliance of Genome Resources, Apr 2022]

ARL10 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 (MetaRNN=0.0010706186).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOP16	NM_016391.8 link	c.*99A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000614830.5	NP_057475.2	Q9Y3C1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOP16	ENST00000614830.5 link	c.*99A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_016391.8	ENSP00000480832.2		Q9Y3C1-1

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16395

AN:

151850

Hom.:

1071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.0783

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.000388

Gnomad SAS

AF:

0.0352

Gnomad FIN

AF:

0.0678

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.0921

Gnomad OTH

AF:

0.112

GnomAD2 exomes

AF:

0.0821

AC:

20274

AN:

246892

AF XY:

0.0817

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.0524

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.000167

Gnomad FIN exome

AF:

0.0687

Gnomad NFE exome

AF:

0.0996

Gnomad OTH exome

AF:

0.0880

GnomAD4 exome

AF:

0.0878

AC:

128246

AN:

1459946

Hom.:

6318

Cov.:

AF XY:

0.0868

AC XY:

63015

AN XY:

726368

show subpopulations

African (AFR)

AF:

0.174

AC:

5832

AN:

33474

American (AMR)

AF:

0.0570

AC:

2547

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

4197

AN:

26134

East Asian (EAS)

AF:

0.000126

AC:

AN:

39698

South Asian (SAS)

AF:

0.0369

AC:

3180

AN:

86240

European-Finnish (FIN)

AF:

0.0700

AC:

3620

AN:

51714

Middle Eastern (MID)

AF:

0.140

AC:

805

AN:

5768

European-Non Finnish (NFE)

AF:

0.0923

AC:

102609

AN:

1111830

Other (OTH)

AF:

0.0903

AC:

5451

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

6623

13247

19870

26494

33117

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.108

AC:

16420

AN:

151968

Hom.:

1074

Cov.:

AF XY:

0.104

AC XY:

7745

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.172

AC:

7135

AN:

41432

American (AMR)

AF:

0.0781

AC:

1194

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

543

AN:

3472

East Asian (EAS)

AF:

0.000389

AC:

AN:

5142

South Asian (SAS)

AF:

0.0358

AC:

172

AN:

4800

European-Finnish (FIN)

AF:

0.0678

AC:

717

AN:

10580

Middle Eastern (MID)

AF:

0.134

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0921

AC:

6255

AN:

67946

Other (OTH)

AF:

0.111

AC:

234

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

721

1442

2163

2884

3605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.105

Hom.:

931

Bravo

AF:

0.112

TwinsUK

AF:

0.0898

AC:

333

ALSPAC

AF:

0.0960

AC:

370

ExAC

AF:

0.0855

AC:

10347

Asia WGS

AF:

0.0290

AC:

101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.1

(source)

DANN

Benign

0.64

DEOGEN2

Benign

0.011

T;T;.

Eigen

Benign

-2.2

Eigen_PC

Benign

-2.3

FATHMM_MKL

Benign

0.0093

LIST_S2

Benign

0.18

T;T;T

MetaRNN

Benign

0.0011

T;T;T

MetaSVM

Benign

-1.1

PhyloP100

-0.50

PrimateAI

Benign

0.26

Sift4G

Benign

0.30

T;T;T

Vest4

0.046

ClinPred

0.0014

GERP RS

-6.0

gMVP

0.060

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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rs1065212

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