rs1004407
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394531.1(WDFY4):c.-18+9079C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,110 control chromosomes in the GnomAD database, including 11,532 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 0.38 ( 11532 hom., cov: 32)
Consequence
WDFY4
NM_001394531.1 intron
NM_001394531.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.919
Genes affected
WDFY4 (HGNC:29323): (WDFY family member 4) Predicted to be involved in autophagy. Predicted to act upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Predicted to act upstream of or within antigen processing and presentation and cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum. [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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDFY4 | NM_001394531.1 | c.-18+9079C>A | intron_variant | ENST00000325239.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDFY4 | ENST00000325239.12 | c.-18+9079C>A | intron_variant | 5 | NM_001394531.1 | P1 | |||
WDFY4 | ENST00000360890.6 | c.-18+9079C>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.379 AC: 57564AN: 151990Hom.: 11507 Cov.: 32
GnomAD3 genomes
?
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151990
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.379 AC: 57636AN: 152110Hom.: 11532 Cov.: 32 AF XY: 0.373 AC XY: 27769AN XY: 74352
GnomAD4 genome
?
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57636
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152110
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32
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27769
AN XY:
74352
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Asia WGS
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1189
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3478
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