chr22-20319694-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_033257.4(DGCR6L):c.216C>T(p.His72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00331 in 1,612,498 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0025 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0034 ( 19 hom. )
Consequence
DGCR6L
NM_033257.4 synonymous
NM_033257.4 synonymous
Scores
16
Clinical Significance
Conservation
PhyloP100: 0.277
Genes affected
DGCR6L (HGNC:18551): (DiGeorge syndrome critical region gene 6 like) This gene, the result of a duplication at this locus, is one of two functional genes encoding nearly identical proteins that have similar expression patterns. The product of this gene is a protein that shares homology with the Drosophila gonadal protein, expressed in gonadal tissues and germ cells, and with the human laminin gamma-1 chain that functions in cell attachment and migration. This gene is located in a region of chromosome 22 implicated in the DiGeorge syndrome, one facet of a broader collection of anomalies referred to as the CATCH 22 syndrome. [provided by RefSeq, Jul 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 (MetaRNN=0.007329792).
BP6
?
Variant 22-20319694-G-A is Benign according to our data. Variant chr22-20319694-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 710255.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.277 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR6L | NM_033257.4 | c.216C>T | p.His72= | synonymous_variant | 2/5 | ENST00000248879.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR6L | ENST00000248879.8 | c.216C>T | p.His72= | synonymous_variant | 2/5 | 1 | NM_033257.4 | P1 | |
DGCR6L | ENST00000443409.1 | c.216C>T | p.His72= | synonymous_variant, NMD_transcript_variant | 2/4 | 1 | |||
DGCR6L | ENST00000405465.3 | c.203C>T | p.Thr68Ile | missense_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00250 AC: 381AN: 152238Hom.: 0 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00262 AC: 652AN: 248510Hom.: 1 AF XY: 0.00266 AC XY: 359AN XY: 134904
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GnomAD4 exome AF: 0.00339 AC: 4956AN: 1460142Hom.: 19 Cov.: 31 AF XY: 0.00344 AC XY: 2499AN XY: 726362
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GnomAD4 genome ? AF: 0.00250 AC: 381AN: 152356Hom.: 0 Cov.: 34 AF XY: 0.00221 AC XY: 165AN XY: 74502
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ClinVar
Significance: Benign/Likely 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 | Invitae | Aug 13, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | DGCR6L: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
GERP RS
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