rs2077579
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004397.6(DDX6):c.*3767A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,896 control chromosomes in the GnomAD database, including 2,486 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 0.17 ( 2486 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
DDX6
NM_004397.6 3_prime_UTR
NM_004397.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.825
Genes affected
DDX6 (HGNC:2747): (DEAD-box helicase 6) This gene encodes a member of the DEAD box protein family. The protein is an RNA helicase found in P-bodies and stress granules, and functions in translation suppression and mRNA degradation. It is required for microRNA-induced gene silencing. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Mar 2012]
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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=-0.58).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX6 | NM_004397.6 | c.*3767A>C | 3_prime_UTR_variant | 14/14 | ENST00000534980.7 | NP_004388.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX6 | ENST00000534980 | c.*3767A>C | 3_prime_UTR_variant | 14/14 | 1 | NM_004397.6 | ENSP00000442266.1 | |||
DDX6 | ENST00000620157 | c.*3767A>C | 3_prime_UTR_variant | 14/14 | 1 | ENSP00000478754.1 | ||||
ENSG00000255422 | ENST00000526274.2 | n.374-1875T>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 26045AN: 151778Hom.: 2482 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
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GnomAD4 genome AF: 0.171 AC: 26049AN: 151896Hom.: 2486 Cov.: 31 AF XY: 0.174 AC XY: 12917AN XY: 74230
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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