rs6136363
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001367614.1(DZANK1):c.1507+6646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,142 control chromosomes in the GnomAD database, including 11,193 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 0.37 ( 11193 hom., cov: 33)
Consequence
DZANK1
NM_001367614.1 intron
NM_001367614.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.225
Genes affected
DZANK1 (HGNC:15858): (double zinc ribbon and ankyrin repeat domains 1) This gene contains two ankyrin repeat-encoding regions. Ankyrin repeats are tandemly repeated modules of about 33 amino acids described as L-shaped structures consisting of a beta-hairpin and two alpha-helices. Ankyrin repeats occur in a large number of functionally diverse proteins, mainly from eukaryotes, and are known to function as protein-protein interaction domains. [provided by RefSeq, Dec 2018]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DZANK1 | NM_001367614.1 | c.1507+6646T>C | intron_variant | ENST00000699568.1 | NP_001354543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DZANK1 | ENST00000699568.1 | c.1507+6646T>C | intron_variant | NM_001367614.1 | ENSP00000514442.1 | |||||
DZANK1 | ENST00000699590.1 | c.1465+6646T>C | intron_variant | ENSP00000514461.1 | ||||||
DZANK1 | ENST00000699525.1 | c.1450+6646T>C | intron_variant | ENSP00000514418.1 | ||||||
DZANK1 | ENST00000357236.8 | c.853+6646T>C | intron_variant | 5 | ENSP00000349774.5 | |||||
DZANK1 | ENST00000480488.2 | c.46+6646T>C | intron_variant | 5 | ENSP00000484666.1 | |||||
DZANK1 | ENST00000377630.9 | n.*638+6646T>C | intron_variant | 2 | ENSP00000366857.6 | |||||
DZANK1 | ENST00000460891.5 | n.*1895+6646T>C | intron_variant | 2 | ENSP00000477872.1 |
Frequencies
GnomAD3 genomes AF: 0.368 AC: 56018AN: 152024Hom.: 11182 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.368 AC: 56036AN: 152142Hom.: 11193 Cov.: 33 AF XY: 0.366 AC XY: 27199AN XY: 74364
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933
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3478
ClinVar
Not reported inComputational scores
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Name
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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