1-92902752-G-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001006605.5(DIPK1A):c.55-26322C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,066 control chromosomes in the GnomAD database, including 39,589 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.71 ( 39589 hom., cov: 31)
Consequence
DIPK1A
NM_001006605.5 intron
NM_001006605.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.411
Genes affected
DIPK1A (HGNC:32213): (divergent protein kinase domain 1A) This gene encodes a member of the FAM69 family of cysteine-rich type II transmembrane proteins. These proteins localize to the endoplasmic reticulum but their specific functions are unknown. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIPK1A | NM_001006605.5 | c.55-26322C>A | intron_variant | ENST00000370310.5 | |||
DIPK1A | NM_001252269.2 | c.55-51797C>A | intron_variant | ||||
DIPK1A | NM_001252270.2 | c.55-26322C>A | intron_variant | ||||
DIPK1A | NM_001252273.2 | c.55-26322C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIPK1A | ENST00000370310.5 | c.55-26322C>A | intron_variant | 2 | NM_001006605.5 | P1 | |||
DIPK1A | ENST00000615519.4 | c.55-26322C>A | intron_variant | 1 | |||||
DIPK1A | ENST00000613902.4 | c.55-51797C>A | intron_variant | 4 | |||||
DIPK1A | ENST00000616709.4 | c.55-26322C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.714 AC: 108471AN: 151948Hom.: 39539 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.714 AC: 108580AN: 152066Hom.: 39589 Cov.: 31 AF XY: 0.717 AC XY: 53303AN XY: 74320
GnomAD4 genome
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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