rs1912453
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394065.1(CCDC190):c.*3264T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,392 control chromosomes in the GnomAD database, including 24,977 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 ( 24967 hom., cov: 28)
Exomes 𝑓: 0.68 ( 10 hom. )
Consequence
CCDC190
NM_001394065.1 3_prime_UTR
NM_001394065.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.362
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=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC190 | NM_001394065.1 | c.*3264T>C | 3_prime_UTR_variant | 4/4 | ENST00000367912.7 | ||
CCDC190 | NM_178550.6 | c.*3264T>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC190 | ENST00000367912.7 | c.*3264T>C | 3_prime_UTR_variant | 4/4 | 5 | NM_001394065.1 | A2 | ||
CCDC190 | ENST00000524691.1 | n.152+4131T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.573 AC: 86653AN: 151230Hom.: 24957 Cov.: 28
GnomAD3 genomes
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GnomAD4 exome AF: 0.682 AC: 30AN: 44Hom.: 10 Cov.: 0 AF XY: 0.706 AC XY: 24AN XY: 34
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GnomAD4 genome ? AF: 0.573 AC: 86702AN: 151348Hom.: 24967 Cov.: 28 AF XY: 0.573 AC XY: 42354AN XY: 73914
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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