rs2270162
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_108105.2(CT66):n.391+254G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 152,312 control chromosomes in the GnomAD database, including 106 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 0.028 ( 106 hom., cov: 33)
Consequence
CT66
NR_108105.2 intron, non_coding_transcript
NR_108105.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.629
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CT66 | NR_108105.2 | n.391+254G>C | intron_variant, non_coding_transcript_variant | ||||
CT66 | NR_148926.1 | n.391+254G>C | intron_variant, non_coding_transcript_variant | ||||
CT66 | NR_148927.1 | n.578+67G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CT66 | ENST00000669908.1 | n.260+254G>C | intron_variant, non_coding_transcript_variant | ||||||
CT66 | ENST00000436600.2 | n.215+254G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0281 AC: 4284AN: 152194Hom.: 107 Cov.: 33
GnomAD3 genomes
?
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152194
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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: 0.0281 AC: 4278AN: 152312Hom.: 106 Cov.: 33 AF XY: 0.0299 AC XY: 2224AN XY: 74476
GnomAD4 genome
?
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4278
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33
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2224
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74476
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186
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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