rs3213654
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005222.4(DLX6):c.*9A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,581,382 control chromosomes in the GnomAD database, including 1,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.037 ( 268 hom., cov: 32)
Exomes 𝑓: 0.012 ( 919 hom. )
Consequence
DLX6
NM_005222.4 3_prime_UTR
NM_005222.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.57
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 7-97010056-A-G is Benign according to our data. Variant chr7-97010056-A-G is described in ClinVar as [Benign]. Clinvar id is 1231769.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLX6 | NM_005222.4 | c.*9A>G | 3_prime_UTR_variant | 3/3 | ENST00000518156.3 | ||
DLX6-AS1 | NR_015448.1 | n.141+3869T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLX6 | ENST00000518156.3 | c.*9A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_005222.4 | P1 | ||
DLX6-AS1 | ENST00000430027.3 | n.141+3869T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0371 AC: 5648AN: 152070Hom.: 261 Cov.: 32
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GnomAD3 exomes AF: 0.0384 AC: 7521AN: 195860Hom.: 414 AF XY: 0.0354 AC XY: 3711AN XY: 104934
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GnomAD4 exome AF: 0.0123 AC: 17627AN: 1429194Hom.: 919 Cov.: 32 AF XY: 0.0127 AC XY: 8964AN XY: 707910
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GnomAD4 genome ? AF: 0.0373 AC: 5683AN: 152188Hom.: 268 Cov.: 32 AF XY: 0.0397 AC XY: 2956AN XY: 74422
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at