22-18906398-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_005675.6(DGCR6):c.24G>A(p.Leu8Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.034 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
DGCR6
NM_005675.6 synonymous
NM_005675.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.232
Genes affected
DGCR6 (HGNC:2846): (DiGeorge syndrome critical region gene 6) DiGeorge syndrome, and more widely, the CATCH 22 syndrome, are associated with microdeletions in chromosomal region 22q11.2. The product of this gene shares homology with the Drosophila melanogaster gonadal protein, which participates in gonadal and germ cell development, and with the gamma-1 subunit of human laminin. This gene is a candidate for involvement in DiGeorge syndrome pathology and in schizophrenia. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 22-18906398-G-A is Benign according to our data. Variant chr22-18906398-G-A is described in ClinVar as [Benign]. Clinvar id is 779194.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.232 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGCR6 | ENST00000331444.12 | c.24G>A | p.Leu8Leu | synonymous_variant | 1/5 | 1 | NM_005675.6 | ENSP00000331681.6 | ||
ENSG00000283809 | ENST00000638240.1 | c.24G>A | p.Leu8Leu | synonymous_variant | 1/6 | 5 | ENSP00000492446.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.00639 AC: 1344AN: 210330Hom.: 43 AF XY: 0.00464 AC XY: 534AN XY: 114994
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0339 AC: 4AN: 118Hom.: 1 Cov.: 0 AF XY: 0.0395 AC XY: 3AN XY: 76
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 0
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 27, 2017 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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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