Variant chrX-45191851-G-T 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_176819.4(DIPK2B):c.398C>A(p.Ala133Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,210,567 control chromosomes in the GnomAD database, including 89 homozygotes. There are 1,101 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 44 hom., 540 hem., cov: 24)

Exomes 𝑓: 0.0019 ( 45 hom. 561 hem. )

Consequence

DIPK2B
NM_176819.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.750

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016578138).

BP6

Variant X-45191851-G-T is Benign according to our data. Variant chrX-45191851-G-T is described in ClinVar as [Benign]. Clinvar id is 718331.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.058 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
DIPK2B	NM_176819.4 linkuse as main transcript	c.398C>A	p.Ala133Glu	missense_variant	2/5	ENST00000398000.7
DIPK2B	NM_024689.3 linkuse as main transcript	c.398C>A	p.Ala133Glu	missense_variant	2/3
DIPK2B	XM_005272670.1 linkuse as main transcript	c.398C>A	p.Ala133Glu	missense_variant	2/4
DIPK2B	XM_006724559.1 linkuse as main transcript	c.398C>A	p.Ala133Glu	missense_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIPK2B	ENST00000398000.7 linkuse as main transcript	c.398C>A	p.Ala133Glu	missense_variant	2/5	5	NM_176819.4	P1	Q9H7Y0-1
	ENST00000450527.5 linkuse as main transcript	n.94+8507G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0174

AC:

1951

AN:

112396

Hom.:

Cov.:

AF XY:

0.0153

AC XY:

530

AN XY:

34556

show subpopulations

Gnomad AFR

AF:

0.0600

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00524

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000367

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00837

Gnomad NFE

AF:

0.000150

Gnomad OTH

AF:

0.0225

GnomAD3 exomes

AF:

0.00517

AC:

947

AN:

183320

Hom.:

AF XY:

0.00335

AC XY:

227

AN XY:

67772

show subpopulations

Gnomad AFR exome

AF:

0.0631

Gnomad AMR exome

AF:

0.00317

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000367

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000171

Gnomad OTH exome

AF:

0.00199

GnomAD4 exome

AF:

0.00193

AC:

2120

AN:

1098117

Hom.:

Cov.:

AF XY:

0.00154

AC XY:

561

AN XY:

363471

show subpopulations

Gnomad4 AFR exome

AF:

0.0629

Gnomad4 AMR exome

AF:

0.00378

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000369

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000127

Gnomad4 OTH exome

AF:

0.00410

GnomAD4 genome

AF:

0.0175

AC:

1963

AN:

112450

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

540

AN XY:

34620

show subpopulations

Gnomad4 AFR

AF:

0.0603

Gnomad4 AMR

AF:

0.00524

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000368

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000150

Gnomad4 OTH

AF:

0.0222

Alfa

AF:

0.00276

Hom.:

Bravo

AF:

0.0201

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.0576

AC:

221

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00568

AC:

690

EpiCase

AF:

0.000327

EpiControl

AF:

0.000237

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

Invitae

Apr 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Uncertain

0.98

FATHMM_MKL

Benign

0.098

LIST_S2

Benign

0.77

T;T

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-0.90

MutationTaster

Benign

1.0

P;P

PROVEAN

Benign

-1.9

N;D

REVEL

Benign

0.080

Sift

Uncertain

0.024

D;D

Sift4G

Uncertain

0.031

D;D

Vest4

0.11

MVP

0.39

MPC

0.63

ClinPred

0.024

GERP RS

-0.41

gMVP

0.76

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