Variant rs4938013 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.453A>C(p.Ile151Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 1,609,924 control chromosomes in the GnomAD database, including 361,510 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 0.69 ( 36202 hom., cov: 32)

Exomes 𝑓: 0.67 ( 325308 hom. )

Consequence

ANKK1
NM_178510.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

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=-0.67).

BP7

Synonymous conserved (PhyloP=-1.11 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKK1	NM_178510.2 link	c.453A>C	p.Ile151Ile	synonymous_variant	2/8	ENST00000303941.4	NP_848605.1	Q8NFD2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKK1	ENST00000303941.4 link	c.453A>C	p.Ile151Ile	synonymous_variant	2/8	1	NM_178510.2	ENSP00000306678.3		Q8NFD2
ANKK1	ENST00000542948.1 link	n.114A>C		non_coding_transcript_exon_variant	1/5	3		ENSP00000445810.1		H0YH32

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104276

AN:

151900

Hom.:

36182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.778

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.673

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.598

Gnomad FIN

AF:

0.669

Gnomad MID

AF:

0.678

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.687

GnomAD3 exomes

AF:

0.638

AC:

156935

AN:

245936

Hom.:

50944

AF XY:

0.641

AC XY:

85635

AN XY:

133516

show subpopulations

Gnomad AFR exome

AF:

0.783

Gnomad AMR exome

AF:

0.486

Gnomad ASJ exome

AF:

0.681

Gnomad EAS exome

AF:

0.565

Gnomad SAS exome

AF:

0.608

Gnomad FIN exome

AF:

0.681

Gnomad NFE exome

AF:

0.672

Gnomad OTH exome

AF:

0.653

GnomAD4 exome

AF:

0.666

AC:

971528

AN:

1457904

Hom.:

325308

Cov.:

AF XY:

0.665

AC XY:

482085

AN XY:

725042

show subpopulations

Gnomad4 AFR exome

AF:

0.777

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.687

Gnomad4 EAS exome

AF:

0.583

Gnomad4 SAS exome

AF:

0.616

Gnomad4 FIN exome

AF:

0.683

Gnomad4 NFE exome

AF:

0.675

Gnomad4 OTH exome

AF:

0.674

GnomAD4 genome

AF:

0.686

AC:

104344

AN:

152020

Hom.:

36202

Cov.:

AF XY:

0.682

AC XY:

50694

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.778

Gnomad4 AMR

AF:

0.585

Gnomad4 ASJ

AF:

0.673

Gnomad4 EAS

AF:

0.566

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.669

Gnomad4 NFE

AF:

0.671

Gnomad4 OTH

AF:

0.683

Alfa

AF:

0.674

Hom.:

59055

Bravo

AF:

0.683

Asia WGS

AF:

0.563

AC:

1956

AN:

3478

EpiCase

AF:

0.674

EpiControl

AF:

0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.8

DANN

Benign

0.67

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