Variant chr11-113399652-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_178510.2(ANKK1):c.1683C>T(p.Tyr561Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 1,601,578 control chromosomes in the GnomAD database, including 533,360 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 0.76 ( 44912 hom., cov: 34)

Exomes 𝑓: 0.82 ( 488448 hom. )

Consequence

ANKK1
NM_178510.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=0.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKK1	NM_178510.2 linkuse as main transcript	c.1683C>T	p.Tyr561Tyr	synonymous_variant	8/8	ENST00000303941.4	NP_848605.1	Q8NFD2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKK1	ENST00000303941.4 linkuse as main transcript	c.1683C>T	p.Tyr561Tyr	synonymous_variant	8/8	1	NM_178510.2	ENSP00000306678.3		Q8NFD2

Frequencies

GnomAD3 genomes

AF:

0.760

AC:

115537

AN:

152056

Hom.:

44889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.876

Gnomad AMR

AF:

0.822

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.961

Gnomad SAS

AF:

0.810

Gnomad FIN

AF:

0.859

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.814

Gnomad OTH

AF:

0.781

GnomAD3 exomes

AF:

0.822

AC:

189081

AN:

229980

Hom.:

78299

AF XY:

0.821

AC XY:

102401

AN XY:

124678

show subpopulations

Gnomad AFR exome

AF:

0.584

Gnomad AMR exome

AF:

0.885

Gnomad ASJ exome

AF:

0.770

Gnomad EAS exome

AF:

0.961

Gnomad SAS exome

AF:

0.818

Gnomad FIN exome

AF:

0.855

Gnomad NFE exome

AF:

0.811

Gnomad OTH exome

AF:

0.818

GnomAD4 exome

AF:

0.819

AC:

1187717

AN:

1449404

Hom.:

488448

Cov.:

AF XY:

0.819

AC XY:

589779

AN XY:

719928

show subpopulations

Gnomad4 AFR exome

AF:

0.571

Gnomad4 AMR exome

AF:

0.878

Gnomad4 ASJ exome

AF:

0.778

Gnomad4 EAS exome

AF:

0.965

Gnomad4 SAS exome

AF:

0.818

Gnomad4 FIN exome

AF:

0.858

Gnomad4 NFE exome

AF:

0.820

Gnomad4 OTH exome

AF:

0.812

GnomAD4 genome

AF:

0.760

AC:

115608

AN:

152174

Hom.:

44912

Cov.:

AF XY:

0.764

AC XY:

56883

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.587

Gnomad4 AMR

AF:

0.823

Gnomad4 ASJ

AF:

0.776

Gnomad4 EAS

AF:

0.961

Gnomad4 SAS

AF:

0.811

Gnomad4 FIN

AF:

0.859

Gnomad4 NFE

AF:

0.814

Gnomad4 OTH

AF:

0.779

Alfa

AF:

0.803

Hom.:

64619

Bravo

AF:

0.754

Asia WGS

AF:

0.829

AC:

2881

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

0.26

DANN

Benign

0.29

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over