rs11604671

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_178510.2(ANKK1):c.952G>A(p.Gly318Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,610,528 control chromosomes in the GnomAD database, including 178,724 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.35 ( 11764 hom., cov: 32)

Exomes 𝑓: 0.47 ( 166960 hom. )

Consequence

ANKK1
NM_178510.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.81

Publications

57 publications found

Variant links:

Genes affected

ANKK1 (HGNC:21027): (ankyrin repeat and kinase domain containing 1) The protein encoded by this gene belongs to the Ser/Thr protein kinase family, and protein kinase superfamily involved in signal transduction pathways. This gene is closely linked to DRD2 gene (GeneID:1813) on chr 11, and a well studied restriction fragment length polymorphism (RFLP) designated TaqIA, was originally associated with the DRD2 gene, however, later was determined to be located in exon 8 of ANKK1 gene (PMIDs: 18621654, 15146457), where it causes a nonconservative amino acid substitution. It is not clear if this gene plays any role in neuropsychiatric disorders previously associated with Taq1A RFLP. [provided by RefSeq, Sep 2009]

ANKK1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.6214725E-5).

BP6

Variant 11-113397337-G-A is Benign according to our data. Variant chr11-113397337-G-A is described in ClinVar as Benign. ClinVar VariationId is 3060965.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKK1	NM_178510.2 link	c.952G>A	p.Gly318Arg	missense_variant	Exon 6 of 8	ENST00000303941.4	NP_848605.1	Q8NFD2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKK1	ENST00000303941.4 link	c.952G>A	p.Gly318Arg	missense_variant	Exon 6 of 8	1	NM_178510.2	ENSP00000306678.3		Q8NFD2

Frequencies

GnomAD3 genomes

AF:

0.351

AC:

53357

AN:

151824

Hom.:

11776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.567

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.483

Gnomad EAS

AF:

0.0609

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.505

Gnomad OTH

AF:

0.395

GnomAD2 exomes

AF:

0.387

AC:

95276

AN:

246430

AF XY:

0.401

show subpopulations

Gnomad AFR exome

AF:

0.0986

Gnomad AMR exome

AF:

0.230

Gnomad ASJ exome

AF:

0.495

Gnomad EAS exome

AF:

0.0579

Gnomad FIN exome

AF:

0.453

Gnomad NFE exome

AF:

0.509

Gnomad OTH exome

AF:

0.440

GnomAD4 exome

AF:

0.465

AC:

678606

AN:

1458586

Hom.:

166960

Cov.:

AF XY:

0.465

AC XY:

337172

AN XY:

725656

show subpopulations

African (AFR)

AF:

0.0972

AC:

3253

AN:

33468

American (AMR)

AF:

0.243

AC:

10861

AN:

44640

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

13034

AN:

26112

East Asian (EAS)

AF:

0.0602

AC:

2390

AN:

39692

South Asian (SAS)

AF:

0.366

AC:

31564

AN:

86186

European-Finnish (FIN)

AF:

0.464

AC:

23977

AN:

51694

Middle Eastern (MID)

AF:

0.431

AC:

2479

AN:

5746

European-Non Finnish (NFE)

AF:

0.508

AC:

564535

AN:

1110766

Other (OTH)

AF:

0.440

AC:

26513

AN:

60282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

17052

34104

51156

68208

85260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15914

31828

47742

63656

79570

<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:

0.351

AC:

53346

AN:

151942

Hom.:

11764

Cov.:

AF XY:

0.345

AC XY:

25642

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.114

AC:

4706

AN:

41440

American (AMR)

AF:

0.301

AC:

4597

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.483

AC:

1675

AN:

3466

East Asian (EAS)

AF:

0.0605

AC:

311

AN:

5144

South Asian (SAS)

AF:

0.340

AC:

1634

AN:

4812

European-Finnish (FIN)

AF:

0.443

AC:

4682

AN:

10564

Middle Eastern (MID)

AF:

0.438

AC:

128

AN:

292

European-Non Finnish (NFE)

AF:

0.505

AC:

34269

AN:

67914

Other (OTH)

AF:

0.393

AC:

828

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1540

3079

4619

6158

7698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.449

Hom.:

24672

Bravo

AF:

0.330

TwinsUK

AF:

0.508

AC:

1885

ALSPAC

AF:

0.519

AC:

2000

ESP6500AA

AF:

0.120

AC:

514

ESP6500EA

AF:

0.503

AC:

4269

ExAC

AF:

0.391

AC:

47409

Asia WGS

AF:

0.182

AC:

634

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ANKK1-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.15

(source)

DANN

Benign

0.67

DEOGEN2

Benign

0.010

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.039

LIST_S2

Benign

0.22

MetaRNN

Benign

0.000046

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.34

PhyloP100

-1.8

PrimateAI

Benign

0.18

PROVEAN

Benign

0.26

REVEL

Benign

0.061

Sift

Benign

0.55

Sift4G

Benign

0.41

Polyphen

0.0

Vest4

0.025

MutPred

0.083

Gain of MoRF binding (P = 0.0254);

MPC

0.070

ClinPred

0.0048

GERP RS

0.52

Varity_R

0.033

gMVP

0.12

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over