Variant 11-113393550-T-C 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.255T>C(p.Ser85Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 1,613,656 control chromosomes in the GnomAD database, including 340,864 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 0.58 ( 26532 hom., cov: 32)

Exomes 𝑓: 0.65 ( 314332 hom. )

Consequence

ANKK1
NM_178510.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.127

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=-0.62).

BP7

Synonymous conserved (PhyloP=0.127 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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.255T>C	p.Ser85Ser	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 linkuse as main transcript	c.255T>C	p.Ser85Ser	synonymous_variant	2/8	1	NM_178510.2	ENSP00000306678.3		Q8NFD2

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

88048

AN:

151914

Hom.:

26528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.781

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.667

Gnomad EAS

AF:

0.565

Gnomad SAS

AF:

0.570

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.631

Gnomad NFE

AF:

0.668

Gnomad OTH

AF:

0.607

GnomAD3 exomes

AF:

0.608

AC:

151292

AN:

249024

Hom.:

47064

AF XY:

0.616

AC XY:

83249

AN XY:

135114

show subpopulations

Gnomad AFR exome

AF:

0.412

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.677

Gnomad EAS exome

AF:

0.565

Gnomad SAS exome

AF:

0.581

Gnomad FIN exome

AF:

0.679

Gnomad NFE exome

AF:

0.670

Gnomad OTH exome

AF:

0.636

GnomAD4 exome

AF:

0.653

AC:

954259

AN:

1461624

Hom.:

314332

Cov.:

AF XY:

0.652

AC XY:

474157

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.407

Gnomad4 AMR exome

AF:

0.482

Gnomad4 ASJ exome

AF:

0.683

Gnomad4 EAS exome

AF:

0.583

Gnomad4 SAS exome

AF:

0.589

Gnomad4 FIN exome

AF:

0.682

Gnomad4 NFE exome

AF:

0.673

Gnomad4 OTH exome

AF:

0.646

GnomAD4 genome

AF:

0.579

AC:

88087

AN:

152032

Hom.:

26532

Cov.:

AF XY:

0.578

AC XY:

42968

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.416

Gnomad4 AMR

AF:

0.541

Gnomad4 ASJ

AF:

0.667

Gnomad4 EAS

AF:

0.565

Gnomad4 SAS

AF:

0.569

Gnomad4 FIN

AF:

0.667

Gnomad4 NFE

AF:

0.668

Gnomad4 OTH

AF:

0.604

Alfa

AF:

0.651

Hom.:

64212

Bravo

AF:

0.562

Asia WGS

AF:

0.527

AC:

1830

AN:

3478

EpiCase

AF:

0.671

EpiControl

AF:

0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

4.8

DANN

Benign

0.40

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