dbSNP rs2296136: ANKRD16:p.Ala128Gly (chr10-5887999-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_019046.3(ANKRD16):c.383C>G(p.Ala128Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 1,614,122 control chromosomes in the GnomAD database, including 1,783 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 ( 165 hom., cov: 32)

Exomes 𝑓: 0.041 ( 1618 hom. )

Consequence

ANKRD16
NM_019046.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.65

Publications

17 publications found

Variant links:

Genes affected

ANKRD16 (HGNC:23471): (ankyrin repeat domain 16) Predicted to be involved in tRNA modification. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD16 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=0.0026624203).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019046.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANKRD16	NM_019046.3	MANE Select	c.383C>G	p.Ala128Gly	missense	Exon 2 of 8	NP_061919.1	Q6P6B7-1
ANKRD16	NM_001009941.3		c.383C>G	p.Ala128Gly	missense	Exon 2 of 7	NP_001009941.1	Q6P6B7-1
ANKRD16	NM_001009943.3		c.383C>G	p.Ala128Gly	missense	Exon 2 of 6	NP_001009943.1	Q6P6B7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANKRD16	ENST00000380094.10	TSL:2 MANE Select	c.383C>G	p.Ala128Gly	missense	Exon 2 of 8	ENSP00000369436.4	Q6P6B7-1
ANKRD16	ENST00000380092.8	TSL:1	c.383C>G	p.Ala128Gly	missense	Exon 2 of 7	ENSP00000369434.4	Q6P6B7-1
ANKRD16	ENST00000958073.1		c.383C>G	p.Ala128Gly	missense	Exon 2 of 8	ENSP00000628132.1

Frequencies

GnomAD3 genomes

AF:

0.0346

AC:

5272

AN:

152176

Hom.:

164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00794

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.0293

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.0877

Gnomad FIN

AF:

0.0751

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0360

Gnomad OTH

AF:

0.0325

GnomAD2 exomes

AF:

0.0527

AC:

13264

AN:

251492

AF XY:

0.0538

show subpopulations

Gnomad AFR exome

AF:

0.00707

Gnomad AMR exome

AF:

0.0539

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.143

Gnomad FIN exome

AF:

0.0690

Gnomad NFE exome

AF:

0.0369

Gnomad OTH exome

AF:

0.0482

GnomAD4 exome

AF:

0.0408

AC:

59581

AN:

1461828

Hom.:

1618

Cov.:

AF XY:

0.0418

AC XY:

30375

AN XY:

727216

show subpopulations

African (AFR)

AF:

0.00597

AC:

200

AN:

33480

American (AMR)

AF:

0.0498

AC:

2228

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0129

AC:

337

AN:

26136

East Asian (EAS)

AF:

0.107

AC:

4262

AN:

39698

South Asian (SAS)

AF:

0.0819

AC:

7062

AN:

86254

European-Finnish (FIN)

AF:

0.0682

AC:

3643

AN:

53412

Middle Eastern (MID)

AF:

0.0160

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0353

AC:

39287

AN:

1111968

Other (OTH)

AF:

0.0409

AC:

2470

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

3430

6860

10291

13721

17151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1582

3164

4746

6328

7910

<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:

0.0347

AC:

5280

AN:

152294

Hom.:

165

Cov.:

AF XY:

0.0380

AC XY:

2832

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.00791

AC:

329

AN:

41578

American (AMR)

AF:

0.0294

AC:

450

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00605

AC:

AN:

3472

East Asian (EAS)

AF:

0.134

AC:

691

AN:

5176

South Asian (SAS)

AF:

0.0871

AC:

420

AN:

4822

European-Finnish (FIN)

AF:

0.0751

AC:

797

AN:

10606

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0360

AC:

2449

AN:

68020

Other (OTH)

AF:

0.0365

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

238

476

715

953

1191

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0315

Hom.:

Bravo

AF:

0.0296

TwinsUK

AF:

0.0359

AC:

133

ALSPAC

AF:

0.0355

AC:

137

ESP6500AA

AF:

0.00999

AC:

ESP6500EA

AF:

0.0349

AC:

300

ExAC

AF:

0.0529

AC:

6417

Asia WGS

AF:

0.130

AC:

449

AN:

3478

EpiCase

AF:

0.0303

EpiControl

AF:

0.0312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Uncertain

-0.080

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.022

Eigen

Uncertain

0.45

Eigen_PC

Uncertain

0.31

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.88

MetaRNN

Benign

0.0027

MetaSVM

Benign

-0.85

MutationAssessor

Uncertain

2.7

PhyloP100

7.6

PrimateAI

Benign

0.46

PROVEAN

Uncertain

-3.8

REVEL

Uncertain

0.33

Sift

Uncertain

0.011

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.28

MPC

0.75

ClinPred

0.021

GERP RS

2.9

Varity_R

0.51

gMVP

0.57

Mutation Taster

=98/2

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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