rs1057239
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014656.3(KIAA0040):c.-55C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 1,479,164 control chromosomes in the GnomAD database, including 142,773 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 0.41 ( 12917 hom., cov: 32)
Exomes 𝑓: 0.44 ( 129856 hom. )
Consequence
KIAA0040
NM_014656.3 5_prime_UTR
NM_014656.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.45
Genes affected
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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=-0.61).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0040 | NM_014656.3 | c.-55C>T | 5_prime_UTR_variant | 4/4 | ENST00000423313.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0040 | ENST00000423313.6 | c.-55C>T | 5_prime_UTR_variant | 4/4 | 1 | NM_014656.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.406 AC: 61626AN: 151882Hom.: 12920 Cov.: 32
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GnomAD4 exome AF: 0.435 AC: 577592AN: 1327162Hom.: 129856 Cov.: 24 AF XY: 0.430 AC XY: 279789AN XY: 650412
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GnomAD4 genome ? AF: 0.406 AC: 61647AN: 152002Hom.: 12917 Cov.: 32 AF XY: 0.402 AC XY: 29864AN XY: 74298
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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