rs7899305
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000447253.1(BTBD7P1):n.526G>A 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 0.283 in 642,818 control chromosomes in the GnomAD database, including 27,645 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 0.29 ( 6628 hom., cov: 29)
Exomes 𝑓: 0.28 ( 21017 hom. )
Consequence
BTBD7P1
ENST00000447253.1 non_coding_transcript_exon
ENST00000447253.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.469
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=-0.63).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 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 |
---|---|---|---|---|---|---|---|---|---|
BTBD7P1 | ENST00000447253.1 | n.526G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.293 AC: 43715AN: 148968Hom.: 6628 Cov.: 29
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GnomAD4 exome AF: 0.280 AC: 138373AN: 493744Hom.: 21017 Cov.: 4 AF XY: 0.278 AC XY: 73344AN XY: 263962
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GnomAD4 genome ? AF: 0.293 AC: 43731AN: 149074Hom.: 6628 Cov.: 29 AF XY: 0.293 AC XY: 21231AN XY: 72574
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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