rs6002616
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The ENST00000396387.2(OLA1P1):n.279T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 1,095,756 control chromosomes in the GnomAD database, including 51,761 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 0.35 ( 9642 hom., cov: 32)
Exomes 𝑓: 0.29 ( 42119 hom. )
Consequence
OLA1P1
ENST00000396387.2 non_coding_transcript_exon
ENST00000396387.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.06
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFA6-DT | NR_034118.2 | n.668-15372A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OLA1P1 | ENST00000396387.2 | n.279T>C | non_coding_transcript_exon_variant | 1/1 | |||||
NDUFA6-DT | ENST00000439129.5 | n.670-15372A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.351 AC: 53282AN: 151936Hom.: 9608 Cov.: 32
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GnomAD4 exome AF: 0.291 AC: 274446AN: 943700Hom.: 42119 Cov.: 17 AF XY: 0.299 AC XY: 146391AN XY: 490174
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GnomAD4 genome ? AF: 0.351 AC: 53363AN: 152056Hom.: 9642 Cov.: 32 AF XY: 0.354 AC XY: 26311AN XY: 74312
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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