rs309244
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000584775.5(CCDC102B):c.-49+530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00696 in 152,068 control chromosomes in the GnomAD database, including 10 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 0.0070 ( 10 hom., cov: 32)
Consequence
CCDC102B
ENST00000584775.5 intron
ENST00000584775.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.593
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=-0.98).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00696 (1058/152068) while in subpopulation AFR AF= 0.0234 (972/41452). AF 95% confidence interval is 0.0222. There are 10 homozygotes in gnomad4. There are 486 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC102B | NM_001093729.2 | c.-49+530G>A | intron_variant | ||||
CCDC102B | XM_017025973.2 | c.-49+530G>A | intron_variant | ||||
CCDC102B | XM_047437804.1 | c.-100+530G>A | intron_variant | ||||
CCDC102B | XM_047437806.1 | c.9+1768G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC102B | ENST00000584775.5 | c.-49+530G>A | intron_variant | 1 | |||||
CCDC102B | ENST00000578970.5 | c.-67+530G>A | intron_variant | 4 | |||||
CCDC102B | ENST00000582371.5 | c.-16+530G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00694 AC: 1055AN: 151952Hom.: 10 Cov.: 32
GnomAD3 genomes
?
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151952
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00696 AC: 1058AN: 152068Hom.: 10 Cov.: 32 AF XY: 0.00654 AC XY: 486AN XY: 74352
GnomAD4 genome
?
AF:
AC:
1058
AN:
152068
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Cov.:
32
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486
AN XY:
74352
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6
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at