rs2305450
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024692.6(CLIP4):c.1534+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,605,518 control chromosomes in the GnomAD database, including 650,446 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 0.88 ( 59630 hom., cov: 32)
Exomes 𝑓: 0.90 ( 590816 hom. )
Consequence
CLIP4
NM_024692.6 intron
NM_024692.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.102
Genes affected
CLIP4 (HGNC:26108): (CAP-Gly domain containing linker protein family member 4) Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Located in intracellular membrane-bounded organelle. [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 (NFE) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLIP4 | NM_024692.6 | c.1534+41G>A | intron_variant | ENST00000320081.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLIP4 | ENST00000320081.10 | c.1534+41G>A | intron_variant | 1 | NM_024692.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.884 AC: 134475AN: 152128Hom.: 59578 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.896 AC: 220732AN: 246486Hom.: 99015 AF XY: 0.892 AC XY: 118670AN XY: 133002
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GnomAD4 exome AF: 0.901 AC: 1309472AN: 1453272Hom.: 590816 Cov.: 30 AF XY: 0.899 AC XY: 649166AN XY: 722252
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GnomAD4 genome ? AF: 0.884 AC: 134584AN: 152246Hom.: 59630 Cov.: 32 AF XY: 0.885 AC XY: 65860AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at