rs1010127
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000479109.2(CCT7P2):n.334T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.408 in 597,550 control chromosomes in the GnomAD database, including 50,551 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 0.40 ( 12494 hom., cov: 32)
Exomes 𝑓: 0.41 ( 38057 hom. )
Consequence
CCT7P2
ENST00000479109.2 non_coding_transcript_exon
ENST00000479109.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.07
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=-0.71).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT7P2 | ENST00000479109.2 | n.334T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.403 AC: 61283AN: 151958Hom.: 12485 Cov.: 32
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GnomAD4 exome AF: 0.409 AC: 182260AN: 445474Hom.: 38057 Cov.: 2 AF XY: 0.410 AC XY: 99080AN XY: 241498
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GnomAD4 genome ? AF: 0.403 AC: 61326AN: 152076Hom.: 12494 Cov.: 32 AF XY: 0.401 AC XY: 29802AN XY: 74318
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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