7-97006051-GGCAGCAGCAGCAGCAGCAGCA-GGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_005222.4(DLX6):c.78_98dupGCAGCAGCAGCAGCAGCAGCA(p.Gln27_Gln33dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000126 in 1,582,054 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 29)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
DLX6
NM_005222.4 disruptive_inframe_insertion
NM_005222.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.11
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_005222.4
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLX6 | NM_005222.4 | c.78_98dupGCAGCAGCAGCAGCAGCAGCA | p.Gln27_Gln33dup | disruptive_inframe_insertion | Exon 1 of 3 | ENST00000518156.3 | NP_005213.3 | |
DLX6-AS1 | NR_015448.1 | n.141+7853_141+7873dupTGCTGCTGCTGCTGCTGCTGC | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000666 AC: 1AN: 150048Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 6.98e-7 AC: 1AN: 1432006Hom.: 0 Cov.: 34 AF XY: 0.00000141 AC XY: 1AN XY: 710120
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GnomAD4 genome AF: 0.00000666 AC: 1AN: 150048Hom.: 0 Cov.: 29 AF XY: 0.0000137 AC XY: 1AN XY: 73220
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at