rs12210761
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_170155.1(OFCC1):n.232-16304C>T 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 0.0374 in 152,224 control chromosomes in the GnomAD database, including 103 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 0.037 ( 103 hom., cov: 33)
Consequence
OFCC1
NR_170155.1 intron, non_coding_transcript
NR_170155.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.989
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=-0.68).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0374 (5692/152224) while in subpopulation SAS AF= 0.0449 (217/4828). AF 95% confidence interval is 0.0417. There are 103 homozygotes in gnomad4. There are 2722 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 101 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OFCC1 | NR_170155.1 | n.232-16304C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000462111.1 | n.164-16304C>T | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000481704.1 | n.232-16304C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0373 AC: 5681AN: 152106Hom.: 101 Cov.: 33
GnomAD3 genomes
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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: 0.0374 AC: 5692AN: 152224Hom.: 103 Cov.: 33 AF XY: 0.0366 AC XY: 2722AN XY: 74440
GnomAD4 genome
?
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33
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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