rs10517368
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001393381.1(CRACD):c.-336+32115A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 152,204 control chromosomes in the GnomAD database, including 127 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 0.029 ( 127 hom., cov: 33)
Consequence
CRACD
NM_001393381.1 intron
NM_001393381.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00300
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRACD | NM_001393381.1 | c.-336+32115A>C | intron_variant | ENST00000682029.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACD | ENST00000682029.1 | c.-336+32115A>C | intron_variant | NM_001393381.1 | A2 | ||||
CRACD | ENST00000629263.3 | c.-493+32115A>C | intron_variant | 5 | |||||
CRACD | ENST00000636006.1 | c.-336+31402A>C | intron_variant | 5 | |||||
CRACD | ENST00000646253.2 | c.-165+31402A>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0285 AC: 4333AN: 152086Hom.: 120 Cov.: 33
GnomAD3 genomes
?
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4333
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152086
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0287 AC: 4364AN: 152204Hom.: 127 Cov.: 33 AF XY: 0.0303 AC XY: 2255AN XY: 74420
GnomAD4 genome
?
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AC:
4364
AN:
152204
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33
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2255
AN XY:
74420
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Asia WGS
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368
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3478
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