Variant X-45200617-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_176819.4(DIPK2B):c.210G>C(p.Lys70Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000398 in 1,210,671 control chromosomes in the GnomAD database, including 3 homozygotes. There are 146 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00064 ( 2 hom., 29 hem., cov: 23)

Exomes 𝑓: 0.00037 ( 1 hom. 117 hem. )

Consequence

DIPK2B
NM_176819.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.17

Variant links:

Genes affected

DIPK2B (HGNC:25866): (divergent protein kinase domain 2B) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

DIPK2B links:

ENSG00000229491 (HGNC:):

ENSG00000229491 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009176999).

BP6

Variant X-45200617-C-G is Benign according to our data. Variant chrX-45200617-C-G is described in ClinVar as [Benign]. Clinvar id is 722221.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000645 (73/113190) while in subpopulation EAS AF= 0.0191 (69/3605). AF 95% confidence interval is 0.0155. There are 2 homozygotes in gnomad4. There are 29 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIPK2B	NM_176819.4 linkuse as main transcript	c.210G>C	p.Lys70Asn	missense_variant	1/5	ENST00000398000.7	NP_789789.2	Q9H7Y0-1Q8WZ11
DIPK2B	NM_024689.3 linkuse as main transcript	c.210G>C	p.Lys70Asn	missense_variant	1/3		NP_078965.2	Q9H7Y0-2
DIPK2B	XM_005272670.1 linkuse as main transcript	c.210G>C	p.Lys70Asn	missense_variant	1/4		XP_005272727.1
DIPK2B	XM_006724559.1 linkuse as main transcript	c.210G>C	p.Lys70Asn	missense_variant	1/4		XP_006724622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DIPK2B	ENST00000398000.7 linkuse as main transcript	c.210G>C	p.Lys70Asn	missense_variant	1/5	5	NM_176819.4	ENSP00000381086.2	Q9H7Y0-1
DIPK2B	ENST00000377934.4 linkuse as main transcript	c.210G>C	p.Lys70Asn	missense_variant	1/3	1		ENSP00000367168.4	Q9H7Y0-2
ENSG00000229491	ENST00000438181.5 linkuse as main transcript	n.179+17188C>G		intron_variant		3
ENSG00000229491	ENST00000450527.5 linkuse as main transcript	n.94+17273C>G		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.000645

AC:

AN:

113139

Hom.:

Cov.:

AF XY:

0.000794

AC XY:

AN XY:

35277

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000186

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0191

Gnomad SAS

AF:

0.000359

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000656

GnomAD3 exomes

AF:

0.00173

AC:

317

AN:

182813

Hom.:

AF XY:

0.00150

AC XY:

101

AN XY:

67393

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0224

Gnomad SAS exome

AF:

0.000211

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000123

Gnomad OTH exome

AF:

0.000444

GnomAD4 exome

AF:

0.000373

AC:

409

AN:

1097481

Hom.:

Cov.:

AF XY:

0.000322

AC XY:

117

AN XY:

362849

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0122

Gnomad4 SAS exome

AF:

0.000166

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000475

Gnomad4 OTH exome

AF:

0.000630

GnomAD4 genome

AF:

0.000645

AC:

AN:

113190

Hom.:

Cov.:

AF XY:

0.000821

AC XY:

AN XY:

35340

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000186

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0191

Gnomad4 SAS

AF:

0.000360

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000649

Alfa

AF:

0.000181

Hom.:

Bravo

AF:

0.000876

ExAC

AF:

0.00154

AC:

187

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.92

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.51

CADD

Uncertain

DANN

Uncertain

1.0

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.84

T;T

MetaRNN

Benign

0.0092

T;T

MetaSVM

Benign

-0.50

PROVEAN

Benign

-1.6

N;D

REVEL

Benign

0.17

Sift

Uncertain

0.017

D;D

Sift4G

Uncertain

0.0080

D;D

Vest4

0.25

MutPred

0.42

Loss of methylation at K70 (P = 2e-04);Loss of methylation at K70 (P = 2e-04);

MVP

0.94

MPC

0.86

ClinPred

0.055

GERP RS

5.1

gMVP

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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