Variant chrX-45191936-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_176819.4(DIPK2B):c.313T>C(p.Ser105Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000885 in 1,210,312 control chromosomes in the GnomAD database, including 6 homozygotes. There are 568 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00050 ( 0 hom., 24 hem., cov: 23)

Exomes 𝑓: 0.00092 ( 6 hom. 544 hem. )

Consequence

DIPK2B
NM_176819.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.867

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007990241).

BP6

Variant X-45191936-A-G is Benign according to our data. Variant chrX-45191936-A-G is described in ClinVar as [Benign]. Clinvar id is 3046016.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 24 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
DIPK2B	NM_176819.4 linkuse as main transcript	c.313T>C	p.Ser105Pro	missense_variant	2/5	ENST00000398000.7
DIPK2B	NM_024689.3 linkuse as main transcript	c.313T>C	p.Ser105Pro	missense_variant	2/3
DIPK2B	XM_005272670.1 linkuse as main transcript	c.313T>C	p.Ser105Pro	missense_variant	2/4
DIPK2B	XM_006724559.1 linkuse as main transcript	c.313T>C	p.Ser105Pro	missense_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIPK2B	ENST00000398000.7 linkuse as main transcript	c.313T>C	p.Ser105Pro	missense_variant	2/5	5	NM_176819.4	P1	Q9H7Y0-1
	ENST00000450527.5 linkuse as main transcript	n.94+8592A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.000490

AC:

AN:

112186

Hom.:

Cov.:

AF XY:

0.000669

AC XY:

AN XY:

34376

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000188

Gnomad ASJ

AF:

0.000378

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00997

Gnomad FIN

AF:

0.000487

Gnomad MID

AF:

0.00422

Gnomad NFE

AF:

0.000394

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00154

AC:

283

AN:

183232

Hom.:

AF XY:

0.00253

AC XY:

171

AN XY:

67694

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000729

Gnomad ASJ exome

AF:

0.000134

Gnomad EAS exome

AF:

0.0000722

Gnomad SAS exome

AF:

0.0126

Gnomad FIN exome

AF:

0.000376

Gnomad NFE exome

AF:

0.000379

Gnomad OTH exome

AF:

0.000442

GnomAD4 exome

AF:

0.000924

AC:

1015

AN:

1098073

Hom.:

Cov.:

AF XY:

0.00150

AC XY:

544

AN XY:

363427

show subpopulations

Gnomad4 AFR exome

AF:

0.0000379

Gnomad4 AMR exome

AF:

0.0000852

Gnomad4 ASJ exome

AF:

0.000310

Gnomad4 EAS exome

AF:

0.0000662

Gnomad4 SAS exome

AF:

0.0126

Gnomad4 FIN exome

AF:

0.000395

Gnomad4 NFE exome

AF:

0.000295

Gnomad4 OTH exome

AF:

0.000976

GnomAD4 genome

AF:

0.000499

AC:

AN:

112239

Hom.:

Cov.:

AF XY:

0.000697

AC XY:

AN XY:

34439

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000188

Gnomad4 ASJ

AF:

0.000378

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0104

Gnomad4 FIN

AF:

0.000487

Gnomad4 NFE

AF:

0.000394

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000407

Hom.:

Bravo

AF:

0.000212

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000297

AC:

ExAC

AF:

0.00211

AC:

256

EpiCase

AF:

0.000491

EpiControl

AF:

0.000712

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

DIPK2B-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 10, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.35

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.46

CADD

Uncertain

DANN

Uncertain

1.0

FATHMM_MKL

Benign

0.73

LIST_S2

Benign

0.77

T;T

MetaRNN

Benign

0.0080

T;T

MetaSVM

Benign

-0.89

MutationTaster

Benign

0.76

N;N

PROVEAN

Benign

-1.5

N;D

REVEL

Benign

0.11

Sift

Benign

0.18

T;D

Sift4G

Benign

0.17

T;D

Vest4

0.16

MVP

0.65

MPC

0.73

ClinPred

0.077

GERP RS

4.3

gMVP

0.77

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