rs6005881
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173510.4(CCDC117):c.*819A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,292 control chromosomes in the GnomAD database, including 16,087 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 0.43 ( 16066 hom., cov: 31)
Exomes 𝑓: 0.37 ( 21 hom. )
Consequence
CCDC117
NM_173510.4 3_prime_UTR
NM_173510.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.185
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC117 | NM_173510.4 | c.*819A>G | 3_prime_UTR_variant | 5/5 | ENST00000249064.9 | ||
CCDC117 | NM_001284263.2 | c.*819A>G | 3_prime_UTR_variant | 4/4 | |||
CCDC117 | NM_001284264.2 | c.*819A>G | 3_prime_UTR_variant | 4/4 | |||
CCDC117 | NM_001284265.1 | c.*819A>G | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC117 | ENST00000249064.9 | c.*819A>G | 3_prime_UTR_variant | 5/5 | 1 | NM_173510.4 | P1 | ||
CCDC117 | ENST00000421503.6 | c.*819A>G | 3_prime_UTR_variant | 4/4 | 2 | ||||
CCDC117 | ENST00000448492.6 | c.*819A>G | 3_prime_UTR_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.429 AC: 65154AN: 151758Hom.: 16015 Cov.: 31
GnomAD3 genomes
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31
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GnomAD4 exome AF: 0.370 AC: 154AN: 416Hom.: 21 Cov.: 0 AF XY: 0.357 AC XY: 90AN XY: 252
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GnomAD4 genome ? AF: 0.430 AC: 65270AN: 151876Hom.: 16066 Cov.: 31 AF XY: 0.432 AC XY: 32028AN XY: 74216
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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