Variant rs1207727 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_005222.4(DLX6):c.437-85A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 1,290,700 control chromosomes in the GnomAD database, including 3,098 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.047 ( 251 hom., cov: 33)

Exomes 𝑓: 0.067 ( 2847 hom. )

Consequence

DLX6
NM_005222.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.12

Variant links:

Genes affected

DLX6 (HGNC:2919): (distal-less homeobox 6) This gene encodes a member of a homeobox transcription factor gene family similiar to the Drosophila distal-less gene. This family is comprised of at least 6 different members that encode proteins with roles in forebrain and craniofacial development. This gene is in a tail-to-tail configuration with another member of the family on the long arm of chromosome 7. [provided by RefSeq, Jul 2008]

DLX6 links:

DLX6-AS1 (HGNC:37151): (DLX6 antisense RNA 1) Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DLX6-AS1 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 (BayesDel_noAF=-0.67).

BP6

Variant 7-97007553-A-C is Benign according to our data. Variant chr7-97007553-A-C is described in ClinVar as [Benign]. Clinvar id is 1225540.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLX6	NM_005222.4 linkuse as main transcript	c.437-85A>C		intron_variant		ENST00000518156.3
DLX6-AS1	NR_015448.1 linkuse as main transcript	n.141+6372T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLX6	ENST00000518156.3 linkuse as main transcript	c.437-85A>C		intron_variant		1	NM_005222.4	P1	P56179-3
DLX6-AS1	ENST00000430027.3 linkuse as main transcript	n.141+6372T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0470

AC:

7154

AN:

152116

Hom.:

251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0129

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.0450

Gnomad ASJ

AF:

0.0288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0747

Gnomad FIN

AF:

0.0394

Gnomad MID

AF:

0.0637

Gnomad NFE

AF:

0.0702

Gnomad OTH

AF:

0.0435

GnomAD3 exomes

AF:

0.0530

AC:

8219

AN:

155208

Hom.:

273

AF XY:

0.0561

AC XY:

4646

AN XY:

82794

show subpopulations

Gnomad AFR exome

AF:

0.0115

Gnomad AMR exome

AF:

0.0353

Gnomad ASJ exome

AF:

0.0308

Gnomad EAS exome

AF:

0.000271

Gnomad SAS exome

AF:

0.0793

Gnomad FIN exome

AF:

0.0449

Gnomad NFE exome

AF:

0.0704

Gnomad OTH exome

AF:

0.0520

GnomAD4 exome

AF:

0.0671

AC:

76390

AN:

1138466

Hom.:

2847

Cov.:

AF XY:

0.0676

AC XY:

38775

AN XY:

573952

show subpopulations

Gnomad4 AFR exome

AF:

0.0127

Gnomad4 AMR exome

AF:

0.0348

Gnomad4 ASJ exome

AF:

0.0318

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0795

Gnomad4 FIN exome

AF:

0.0449

Gnomad4 NFE exome

AF:

0.0744

Gnomad4 OTH exome

AF:

0.0618

GnomAD4 genome

AF:

0.0470

AC:

7155

AN:

152234

Hom.:

251

Cov.:

AF XY:

0.0453

AC XY:

3374

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0128

Gnomad4 AMR

AF:

0.0449

Gnomad4 ASJ

AF:

0.0288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0756

Gnomad4 FIN

AF:

0.0394

Gnomad4 NFE

AF:

0.0702

Gnomad4 OTH

AF:

0.0430

Alfa

AF:

0.0531

Hom.:

Bravo

AF:

0.0458

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

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

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

9.6

DANN

Benign

0.82

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