rs7118900

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP6BA1

The NM_178510.2(ANKK1):c.715G>A(p.Ala239Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,613,786 control chromosomes in the GnomAD database, including 39,971 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.25 ( 5101 hom., cov: 32)

Exomes 𝑓: 0.21 ( 34870 hom. )

Consequence

ANKK1
NM_178510.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.00

Publications

62 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 -9 ACMG points.

BP6

Variant 11-113396099-G-A is Benign according to our data. Variant chr11-113396099-G-A is described in ClinVar as Benign. ClinVar VariationId is 3060698.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKK1	NM_178510.2 link	c.715G>A	p.Ala239Thr	missense_variant	Exon 5 of 8	ENST00000303941.4	NP_848605.1	Q8NFD2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKK1	ENST00000303941.4 link	c.715G>A	p.Ala239Thr	missense_variant	Exon 5 of 8	1	NM_178510.2	ENSP00000306678.3	Q8NFD2
ANKK1	ENST00000542948.1 link	n.*269G>A		non_coding_transcript_exon_variant	Exon 5 of 5	3		ENSP00000445810.1	H0YH32
ANKK1	ENST00000542948.1 link	n.*269G>A		3_prime_UTR_variant	Exon 5 of 5	3		ENSP00000445810.1	H0YH32

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37472

AN:

152018

Hom.:

5089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.232

GnomAD2 exomes

AF:

0.253

AC:

63155

AN:

249136

AF XY:

0.243

show subpopulations

Gnomad AFR exome

AF:

0.324

Gnomad AMR exome

AF:

0.449

Gnomad ASJ exome

AF:

0.134

Gnomad EAS exome

AF:

0.398

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.180

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.208

AC:

304222

AN:

1461650

Hom.:

34870

Cov.:

AF XY:

0.208

AC XY:

151413

AN XY:

727116

show subpopulations

African (AFR)

AF:

0.313

AC:

10488

AN:

33478

American (AMR)

AF:

0.428

AC:

19156

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.133

AC:

3479

AN:

26134

East Asian (EAS)

AF:

0.384

AC:

15255

AN:

39700

South Asian (SAS)

AF:

0.274

AC:

23667

AN:

86254

European-Finnish (FIN)

AF:

0.183

AC:

9752

AN:

53378

Middle Eastern (MID)

AF:

0.153

AC:

880

AN:

5768

European-Non Finnish (NFE)

AF:

0.188

AC:

208936

AN:

1111844

Other (OTH)

AF:

0.209

AC:

12609

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

13625

27251

40876

54502

68127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7728

15456

23184

30912

38640

<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:

0.247

AC:

37519

AN:

152136

Hom.:

5101

Cov.:

AF XY:

0.249

AC XY:

18554

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.324

AC:

13430

AN:

41484

American (AMR)

AF:

0.321

AC:

4906

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

534

AN:

3472

East Asian (EAS)

AF:

0.397

AC:

2043

AN:

5150

South Asian (SAS)

AF:

0.285

AC:

1377

AN:

4824

European-Finnish (FIN)

AF:

0.194

AC:

2060

AN:

10594

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12501

AN:

68004

Other (OTH)

AF:

0.233

AC:

492

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1436

2872

4307

5743

7179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.205

Hom.:

16531

Bravo

AF:

0.262

TwinsUK

AF:

0.186

AC:

690

ALSPAC

AF:

0.176

AC:

680

ESP6500AA

AF:

0.308

AC:

1246

ESP6500EA

AF:

0.182

AC:

1518

ExAC

AF:

0.246

AC:

29698

Asia WGS

AF:

0.340

AC:

1182

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 21, 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

0.10

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.071

Eigen

Benign

-0.98

Eigen_PC

Benign

-0.96

FATHMM_MKL

Uncertain

0.84

LIST_S2

Benign

0.25

MetaRNN

Benign

0.00050

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.0

PhyloP100

2.0

PrimateAI

Benign

0.31

PROVEAN

Benign

-1.1

REVEL

Benign

0.21

Sift

Benign

0.11

Sift4G

Uncertain

0.039

Polyphen

0.15

Vest4

0.099

MPC

0.068

ClinPred

0.018

GERP RS

2.5

Varity_R

0.033

gMVP

0.26

Mutation Taster

=80/20

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.30

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.30

Position offset: 27

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