rs861857
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 22-21628051-C-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 183,204 control chromosomes in the GnomAD database, including 23,891 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 0.51 ( 20669 hom., cov: 33)
Exomes 𝑓: 0.44 ( 3222 hom. )
Consequence
YDJC
NM_001017964.2 downstream_gene
NM_001017964.2 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0440
Genes affected
YDJC (HGNC:27158): (YdjC chitooligosaccharide deacetylase homolog) Predicted to enable deacetylase activity and magnesium ion binding activity. Predicted to be involved in carbohydrate metabolic process. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YDJC | NM_001017964.2 | downstream_gene_variant | ENST00000292778.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YDJC | ENST00000292778.11 | downstream_gene_variant | 2 | NM_001017964.2 | P1 | ||||
YDJC | ENST00000415762.6 | downstream_gene_variant | 1 | ||||||
YDJC | ENST00000464015.5 | downstream_gene_variant | 1 | ||||||
YDJC | ENST00000468686.5 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.512 AC: 77773AN: 151932Hom.: 20618 Cov.: 33
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GnomAD4 exome AF: 0.444 AC: 13824AN: 31154Hom.: 3222 Cov.: 0 AF XY: 0.439 AC XY: 6834AN XY: 15550
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GnomAD4 genome ? AF: 0.512 AC: 77886AN: 152050Hom.: 20669 Cov.: 33 AF XY: 0.516 AC XY: 38325AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at