rs7249735
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000595391.1(CYP2A7P1):n.495T>G 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 0.312 in 773,298 control chromosomes in the GnomAD database, including 40,571 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 0.33 ( 8582 hom., cov: 31)
Exomes 𝑓: 0.31 ( 31989 hom. )
Consequence
CYP2A7P1
ENST00000595391.1 non_coding_transcript_exon
ENST00000595391.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.97
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 (AMR) allele frequency at 95% confidence interval = 0.416 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 |
---|---|---|---|---|---|---|---|---|---|
CYP2A7P1 | ENST00000595391.1 | n.495T>G | non_coding_transcript_exon_variant | 4/5 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49587AN: 151610Hom.: 8580 Cov.: 31
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GnomAD3 exomes AF: 0.323 AC: 80751AN: 250132Hom.: 14101 AF XY: 0.322 AC XY: 43543AN XY: 135170
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GnomAD4 exome AF: 0.309 AC: 191968AN: 621570Hom.: 31989 Cov.: 3 AF XY: 0.312 AC XY: 105748AN XY: 338428
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GnomAD4 genome ? AF: 0.327 AC: 49614AN: 151728Hom.: 8582 Cov.: 31 AF XY: 0.326 AC XY: 24130AN XY: 74102
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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