7-97006051-GGCAGCAGCAGCAGCAGCAGCA-GGCA
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005222.4(DLX6):c.81_98delGCAGCAGCAGCAGCAGCA(p.Gln28_Gln33del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000107 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 0.000027 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000091 ( 0 hom. )
Consequence
DLX6
NM_005222.4 disruptive_inframe_deletion
NM_005222.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.66
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 Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLX6 | NM_005222.4 | c.81_98delGCAGCAGCAGCAGCAGCA | p.Gln28_Gln33del | disruptive_inframe_deletion | Exon 1 of 3 | ENST00000518156.3 | NP_005213.3 | |
DLX6-AS1 | NR_015448.1 | n.141+7856_141+7873delTGCTGCTGCTGCTGCTGC | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 4AN: 150048Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00000908 AC: 13AN: 1432006Hom.: 0 AF XY: 0.00000845 AC XY: 6AN XY: 710120
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GnomAD4 genome AF: 0.0000267 AC: 4AN: 150048Hom.: 0 Cov.: 29 AF XY: 0.0000273 AC XY: 2AN XY: 73220
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ClinVar
Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at