chr7-97008925-A-G

Variant names:

• chr7-97008925-A-G
• rs3801290
• NM_005222.4:c.631-871A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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: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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005222.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6	NM_005222.4	MANE Select	c.631-871A>G		intron	N/A	NP_005213.3
	DLX6-AS1	NR_015448.1		n.141+5000T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6	ENST00000518156.3	TSL:1 MANE Select	c.631-871A>G		intron	N/A	ENSP00000428480.2
	DLX6-AS1	ENST00000458352.5	TSL:1	n.615+2900T>C		intron	N/A
	DLX6	ENST00000555308.1	TSL:2	c.247-871A>G		intron	N/A	ENSP00000451635.1

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

African (AFR) AF: 0.318 AC: 13196 AN: 41486

American (AMR) AF: 0.414 AC: 6326 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1427 AN: 5184

South Asian (SAS) AF: 0.224 AC: 1083 AN: 4832

European-Finnish (FIN) AF: 0.301 AC: 3186 AN: 10594

Middle Eastern (MID) AF: 0.310 AC: 90 AN: 290

European-Non Finnish (NFE) AF: 0.317 AC: 21529 AN: 67998

Other (OTH) AF: 0.324 AC: 685 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.37
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3801290; hg19: chr7-96638237;