rs7724774
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015621.3(CCDC69):c.49-831C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,240 control chromosomes in the GnomAD database, including 677 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 0.085 ( 677 hom., cov: 31)
Consequence
CCDC69
NM_015621.3 intron
NM_015621.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.365
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC69 | NM_015621.3 | c.49-831C>T | intron_variant | ENST00000355417.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC69 | ENST00000355417.7 | c.49-831C>T | intron_variant | 1 | NM_015621.3 | P1 | |||
CCDC69 | ENST00000521308.5 | n.172-4618C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
CCDC69 | ENST00000522179.1 | n.491-831C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0850 AC: 12932AN: 152122Hom.: 673 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0850 AC: 12943AN: 152240Hom.: 677 Cov.: 31 AF XY: 0.0852 AC XY: 6341AN XY: 74436
GnomAD4 genome
?
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AC:
12943
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152240
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31
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6341
AN XY:
74436
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Asia WGS
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311
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3478
ClinVar
Not reported inComputational scores
Source:
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