rs8061107
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014157.4(CCDC113):c.891+339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,556 control chromosomes in the GnomAD database, including 26,985 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 0.59 ( 26985 hom., cov: 29)
Consequence
CCDC113
NM_014157.4 intron
NM_014157.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.385
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 (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC113 | NM_014157.4 | c.891+339C>T | intron_variant | ENST00000219299.8 | |||
CCDC113 | NM_001142302.2 | c.729+339C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC113 | ENST00000219299.8 | c.891+339C>T | intron_variant | 1 | NM_014157.4 | P1 | |||
CCDC113 | ENST00000443128.6 | c.729+339C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.585 AC: 88629AN: 151436Hom.: 26966 Cov.: 29
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.585 AC: 88688AN: 151556Hom.: 26985 Cov.: 29 AF XY: 0.574 AC XY: 42496AN XY: 73978
GnomAD4 genome
?
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88688
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151556
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29
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42496
AN XY:
73978
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1568
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3478
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