Variant rs3213654 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005222.4(DLX6):c.*9A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,581,382 control chromosomes in the GnomAD database, including 1,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 268 hom., cov: 32)

Exomes 𝑓: 0.012 ( 919 hom. )

Consequence

DLX6
NM_005222.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.57

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 7-97010056-A-G is Benign according to our data. Variant chr7-97010056-A-G is described in ClinVar as [Benign]. Clinvar id is 1231769.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLX6	NM_005222.4 linkuse as main transcript	c.*9A>G		3_prime_UTR_variant	3/3	ENST00000518156.3	NP_005213.3
DLX6-AS1	NR_015448.1 linkuse as main transcript	n.141+3869T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX6	ENST00000518156.3 linkuse as main transcript	c.*9A>G		3_prime_UTR_variant	3/3	1	NM_005222.4	ENSP00000428480	P1	P56179-3
DLX6-AS1	ENST00000430027.3 linkuse as main transcript	n.141+3869T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0371

AC:

5648

AN:

152070

Hom.:

261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0772

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0878

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.0519

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000765

Gnomad OTH

AF:

0.0377

GnomAD3 exomes

AF:

0.0384

AC:

7521

AN:

195860

Hom.:

414

AF XY:

0.0354

AC XY:

3711

AN XY:

104934

show subpopulations

Gnomad AFR exome

AF:

0.0806

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.000992

Gnomad EAS exome

AF:

0.147

Gnomad SAS exome

AF:

0.0480

Gnomad FIN exome

AF:

0.000159

Gnomad NFE exome

AF:

0.000438

Gnomad OTH exome

AF:

0.0233

GnomAD4 exome

AF:

0.0123

AC:

17627

AN:

1429194

Hom.:

919

Cov.:

AF XY:

0.0127

AC XY:

8964

AN XY:

707910

show subpopulations

Gnomad4 AFR exome

AF:

0.0761

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.000942

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.0460

Gnomad4 FIN exome

AF:

0.000116

Gnomad4 NFE exome

AF:

0.000227

Gnomad4 OTH exome

AF:

0.0216

GnomAD4 genome

AF:

0.0373

AC:

5683

AN:

152188

Hom.:

268

Cov.:

AF XY:

0.0397

AC XY:

2956

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0772

Gnomad4 AMR

AF:

0.0886

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.0517

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000765

Gnomad4 OTH

AF:

0.0421

Alfa

AF:

0.0128

Hom.:

Bravo

AF:

0.0451

Asia WGS

AF:

0.130

AC:

451

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

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