rs284856
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001083913.2(WBP1L):c.*1241A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 148,536 control chromosomes in the GnomAD database, including 24,158 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 0.57 ( 24079 hom., cov: 23)
Exomes 𝑓: 0.58 ( 79 hom. )
Consequence
WBP1L
NM_001083913.2 3_prime_UTR
NM_001083913.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.363
Genes affected
WBP1L (HGNC:23510): (WW domain binding protein 1 like) Predicted to enable ubiquitin protein ligase binding activity. Predicted to act upstream of or within CXCL12-activated CXCR4 signaling pathway; hemopoiesis; and positive regulation of protein ubiquitination. Predicted to be integral component of membrane. [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=-0.64).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WBP1L | NM_001083913.2 | c.*1241A>T | 3_prime_UTR_variant | 4/4 | ENST00000448841.7 | ||
WBP1L | NM_017787.5 | c.*1241A>T | 3_prime_UTR_variant | 4/4 | |||
WBP1L | XM_011539913.3 | c.*1241A>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WBP1L | ENST00000448841.7 | c.*1241A>T | 3_prime_UTR_variant | 4/4 | 2 | NM_001083913.2 | A2 | ||
WBP1L | ENST00000369889.5 | c.*1241A>T | 3_prime_UTR_variant | 4/4 | 1 | P4 | |||
WBP1L | ENST00000647664.1 | c.355+4518A>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.569 AC: 84278AN: 147998Hom.: 24060 Cov.: 23
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GnomAD4 exome AF: 0.584 AC: 250AN: 428Hom.: 79 Cov.: 0 AF XY: 0.605 AC XY: 155AN XY: 256
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GnomAD4 genome ? AF: 0.569 AC: 84342AN: 148108Hom.: 24079 Cov.: 23 AF XY: 0.573 AC XY: 41197AN XY: 71884
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ClinVar
Not reported inComputational scores
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Name
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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