rs7739
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001375834.1(WIPF1):c.*2846C>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 0.914 in 152,514 control chromosomes in the GnomAD database, including 63,914 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 0.91 ( 63754 hom., cov: 30)
Exomes 𝑓: 0.94 ( 160 hom. )
Consequence
WIPF1
NM_001375834.1 3_prime_UTR
NM_001375834.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.55
Genes affected
WIPF1 (HGNC:12736): (WAS/WASL interacting protein family member 1) This gene encodes a protein that plays an important role in the organization of the actin cytoskeleton. The encoded protein binds to a region of Wiskott-Aldrich syndrome protein that is frequently mutated in Wiskott-Aldrich syndrome, an X-linked recessive disorder. Impairment of the interaction between these two proteins may contribute to the disease. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WIPF1 | NM_001375834.1 | c.*2846C>T | 3_prime_UTR_variant | 8/8 | ENST00000679041.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WIPF1 | ENST00000679041.1 | c.*2846C>T | 3_prime_UTR_variant | 8/8 | NM_001375834.1 | P3 | |||
ENST00000442996.1 | n.217+12224G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.914 AC: 138999AN: 152032Hom.: 63716 Cov.: 30
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GnomAD4 exome AF: 0.937 AC: 341AN: 364Hom.: 160 Cov.: 0 AF XY: 0.932 AC XY: 207AN XY: 222
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GnomAD4 genome ? AF: 0.914 AC: 139089AN: 152150Hom.: 63754 Cov.: 30 AF XY: 0.914 AC XY: 67953AN XY: 74374
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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