rs3801290

Positions:

• chr7-97008925-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005222.4(DLX6):​c.631-871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,168 control chromosomes in the GnomAD database, including 8,015 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 0.32 (8015 hom., cov: 33)
• Consequence: DLX6 NM_005222.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLX6	NM_005222.4	c.631-871A>G		intron_variant		ENST00000518156.3	NP_005213.3
DLX6-AS1	NR_015448.1	n.141+5000T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX6	ENST00000518156.3	c.631-871A>G		intron_variant		1	NM_005222.4	ENSP00000428480.2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 49019 AN: 152050 Hom.: 8018 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.322 AC: 49047 AN: 152168 Hom.: 8015 Cov.: 33 AF XY: 0.321 AC XY: 23886 AN XY: 74384

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.324

Alfa AF: 0.314 Hom.: 934

Bravo AF: 0.337

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.37

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

Other links and lift over

dbSNP: rs3801290; hg19: chr7-96638237;