Variant rs2228184 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004405.4(DLX2):c.525A>G(p.Gln175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,613,662 control chromosomes in the GnomAD database, including 132,059 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 10007 hom., cov: 34)

Exomes 𝑓: 0.40 ( 122052 hom. )

Consequence

DLX2
NM_004405.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Variant links:

Genes affected

DLX2 (HGNC:2915): (distal-less homeobox 2) Many vertebrate homeo box-containing genes have been identified on the basis of their sequence similarity with Drosophila developmental genes. Members of the Dlx gene family contain a homeobox that is related to that of Distal-less (Dll), a gene expressed in the head and limbs of the developing fruit fly. The Distal-less (Dlx) family of genes comprises at least 6 different members, DLX1-DLX6. The DLX proteins are postulated to play a role in forebrain and craniofacial development. This gene is located in a tail-to-tail configuration with another member of the gene family on the long arm of chromosome 2. [provided by RefSeq, Jul 2008]

DLX2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP7

Synonymous conserved (PhyloP=-0.04 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLX2	NM_004405.4 linkuse as main transcript	c.525A>G	p.Gln175=	synonymous_variant	2/3	ENST00000234198.9	NP_004396.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX2	ENST00000234198.9 linkuse as main transcript	c.525A>G	p.Gln175=	synonymous_variant	2/3	1	NM_004405.4	ENSP00000234198	P1	Q07687-1
DLX2	ENST00000466293.2 linkuse as main transcript	c.525A>G	p.Gln175=	synonymous_variant	2/2	2		ENSP00000446904		Q07687-2

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51375

AN:

152084

Hom.:

9991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.327

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.469

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.408

Gnomad OTH

AF:

0.333

GnomAD3 exomes

AF:

0.401

AC:

100301

AN:

249896

Hom.:

21207

AF XY:

0.410

AC XY:

55456

AN XY:

135354

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.340

Gnomad ASJ exome

AF:

0.312

Gnomad EAS exome

AF:

0.632

Gnomad SAS exome

AF:

0.425

Gnomad FIN exome

AF:

0.463

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.380

GnomAD4 exome

AF:

0.404

AC:

590718

AN:

1461460

Hom.:

122052

Cov.:

AF XY:

0.406

AC XY:

295053

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.334

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.609

Gnomad4 SAS exome

AF:

0.434

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.406

Gnomad4 OTH exome

AF:

0.384

GnomAD4 genome

AF:

0.338

AC:

51418

AN:

152202

Hom.:

10007

Cov.:

AF XY:

0.346

AC XY:

25733

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.328

Gnomad4 ASJ

AF:

0.306

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.426

Gnomad4 FIN

AF:

0.469

Gnomad4 NFE

AF:

0.408

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.382

Hom.:

15233

Bravo

AF:

0.319

Asia WGS

AF:

0.464

AC:

1617

AN:

3478

EpiCase

AF:

0.395

EpiControl

AF:

0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.0

DANN

Benign

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over