Variant chr7-140681083-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000072869.9(ADCK2):c.1251C>T(p.Pro417=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,614,070 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0020 ( 2 hom. )

Consequence

ADCK2
ENST00000072869.9 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.47

Variant links:

Genes affected

ADCK2 (HGNC:19039): (aarF domain containing kinase 2) Predicted to enable ATP binding activity and protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ADCK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 7-140681083-C-T is Benign according to our data. Variant chr7-140681083-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658022.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.47 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ADCK2	NM_052853.4 linkuse as main transcript	c.1251C>T	p.Pro417=	synonymous_variant	4/8	ENST00000072869.9	NP_443085.2
ADCK2	XM_006716170.5 linkuse as main transcript	c.1251C>T	p.Pro417=	synonymous_variant	4/7		XP_006716233.1
ADCK2	XM_011516675.4 linkuse as main transcript	c.1209+1800C>T		intron_variant			XP_011514977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCK2	ENST00000072869.9 linkuse as main transcript	c.1251C>T	p.Pro417=	synonymous_variant	4/8	1	NM_052853.4	ENSP00000072869	P1

Frequencies

GnomAD3 genomes

AF:

0.00173

AC:

263

AN:

152082

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00232

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00187

AC:

469

AN:

251468

Hom.:

AF XY:

0.00185

AC XY:

251

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.00301

Gnomad ASJ exome

AF:

0.00387

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00108

Gnomad FIN exome

AF:

0.000924

Gnomad NFE exome

AF:

0.00223

Gnomad OTH exome

AF:

0.00293

GnomAD4 exome

AF:

0.00202

AC:

2954

AN:

1461870

Hom.:

Cov.:

AF XY:

0.00208

AC XY:

1510

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.000508

Gnomad4 AMR exome

AF:

0.00257

Gnomad4 ASJ exome

AF:

0.00436

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00123

Gnomad4 FIN exome

AF:

0.00118

Gnomad4 NFE exome

AF:

0.00217

Gnomad4 OTH exome

AF:

0.00190

GnomAD4 genome

AF:

0.00176

AC:

268

AN:

152200

Hom.:

Cov.:

AF XY:

0.00167

AC XY:

124

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.000385

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00232

Gnomad4 OTH

AF:

0.00380

Alfa

AF:

0.00219

Hom.:

Bravo

AF:

0.00160

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00224

EpiControl

AF:

0.00231

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

ADCK2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

0.68

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over