Genetic Variant DLX1:c.*453G>A (chr2-172088710-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178120.5(DLX1):c.*453G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 153,648 control chromosomes in the GnomAD database, including 15,079 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 0.41 ( 14952 hom., cov: 34)

Exomes 𝑓: 0.36 ( 127 hom. )

Consequence

DLX1
NM_178120.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

14 publications found

Variant links:

Genes affected

DLX1 (HGNC:2914): (distal-less homeobox 1) This gene encodes a member of a homeobox transcription factor gene family similiar to the Drosophila distal-less gene. The encoded protein is localized to the nucleus where it may function as a transcriptional regulator of signals from multiple TGF-{beta} superfamily members. The encoded protein may play a role in the control of craniofacial patterning and the differentiation and survival of inhibitory neurons in the forebrain. This gene is located in a tail-to-tail configuration with another member of the family on the long arm of chromosome 2. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

DLX1 links:

ENSG00000288958 (HGNC:):

ENSG00000288958 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLX1	NM_178120.5 link	c.*453G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000361725.5	NP_835221.2	P56177-1X5D2F9
DLX1	NM_001038493.2 link	c.*631G>A		3_prime_UTR_variant	Exon 2 of 2		NP_001033582.1	P56177-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DLX1	ENST00000361725.5 link	c.*453G>A	3_prime_UTR_variant	Exon 3 of 3	1	NM_178120.5	ENSP00000354478.4	P56177-1
DLX1	ENST00000341900.6 link	c.*631G>A	3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000341786.6	P56177-2
DLX1	ENST00000475989.2 link	n.1295G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000288958	ENST00000715284.1 link	n.308+4630C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

62972

AN:

151820

Hom.:

14930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.329

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.402

GnomAD4 exome

AF:

0.360

AC:

615

AN:

1710

Hom.:

127

Cov.:

AF XY:

0.340

AC XY:

323

AN XY:

950

show subpopulations

African (AFR)

AF:

0.671

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.538

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.361

AC:

164

AN:

454

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.324

AC:

303

AN:

936

Other (OTH)

AF:

0.378

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.415

AC:

63040

AN:

151938

Hom.:

14952

Cov.:

AF XY:

0.409

AC XY:

30396

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.660

AC:

27307

AN:

41368

American (AMR)

AF:

0.314

AC:

4791

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1333

AN:

3470

East Asian (EAS)

AF:

0.222

AC:

1153

AN:

5186

South Asian (SAS)

AF:

0.302

AC:

1454

AN:

4822

European-Finnish (FIN)

AF:

0.349

AC:

3684

AN:

10554

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.325

AC:

22081

AN:

67948

Other (OTH)

AF:

0.403

AC:

849

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1773

3546

5320

7093

8866

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.348

Hom.:

43482

Bravo

AF:

0.425

Asia WGS

AF:

0.331

AC:

1151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.9

(source)

DANN

Benign

0.88

PhyloP100

0.082

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over