Variant rs1800497 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_178510.2(ANKK1):c.2137G>A(p.Glu713Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152052 control chromosomes in the gnomAD Genomes database, including 5529 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5529 hom., cov: 34)

Exomes 𝑓: 0.26 ( 9971 hom. )

Consequence

ANKK1
NM_178510.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.438

Links

ANKK1 (HGNC:21027):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.9350004E-4).

BP6

Variant 11-113400106-G-A is Benign according to our data. Variant chr11-113400106-G-A is described in ClinVar as [Benign]. Clinvar id is 2105. Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKK1	NM_178510.2 linkuse as main transcript	c.2137G>A	p.Glu713Lys	missense_variant	8/8	ENST00000303941.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKK1	ENST00000303941.4 linkuse as main transcript	c.2137G>A	p.Glu713Lys	missense_variant	8/8	1	NM_178510.2	P1

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39295

AN:

152052

Hom.:

5529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.169

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.246

GnomAD3 exomes

AF:

0.264

AC:

65225

AN:

246888

Hom.:

9971

AF XY:

0.254

AC XY:

34091

AN XY:

134200

show subpopulations

Gnomad AFR exome

AF:

0.345

Gnomad AMR exome

AF:

0.449

Gnomad ASJ exome

AF:

0.149

Gnomad EAS exome

AF:

0.400

Gnomad SAS exome

AF:

0.289

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.192

Gnomad OTH exome

AF:

0.223

GnomAD4 exome

AF:

0.219

AC:

320284

AN:

1460472

Hom.:

38093

AF XY:

0.219

AC XY:

159389

AN XY:

726500

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.428

Gnomad4 ASJ exome

AF:

0.148

Gnomad4 EAS exome

AF:

0.384

Gnomad4 SAS exome

AF:

0.283

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.199

Gnomad4 OTH exome

AF:

0.221

Alfa

AF:

0.207

Hom.:

5053

Bravo

AF:

0.273

TwinsUK

AF:

0.195

AC:

723

ALSPAC

AF:

0.186

AC:

718

ESP6500AA

AF:

0.327

AC:

1351

ESP6500EA

AF:

0.190

AC:

1598

ExAC

AF:

0.256

AC:

31010

Asia WGS

AF:

0.347

AC:

1207

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Apr 16, 2013

- -

Taq1A POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Oct 17, 2008

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.053

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

Cadd

Benign

4.8

Dann

Benign

0.17

DEOGEN2

Benign

0.0055

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.22

MetaRNN

Benign

0.00069

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.93

MutationTaster

Benign

1.0

PrimateAI

Benign

0.31

PROVEAN

Benign

0.86

REVEL

Benign

0.059

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.056

MPC

0.066

ClinPred

0.0026

GERP RS

2.0

Varity_R

0.038

gMVP

0.12

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over