rs4459610
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000423435.2(ACE3P):n.58-205A>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 0.54 in 398,798 control chromosomes in the GnomAD database, including 60,001 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 0.54 ( 22985 hom., cov: 32)
Exomes 𝑓: 0.54 ( 37016 hom. )
Consequence
ACE3P
ENST00000423435.2 intron, non_coding_transcript
ENST00000423435.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.117
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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 |
---|---|---|---|---|---|---|---|---|---|
ACE3P | ENST00000423435.2 | n.58-205A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.544 AC: 82666AN: 151888Hom.: 22965 Cov.: 32
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GnomAD3 exomes AF: 0.552 AC: 4845AN: 8782Hom.: 1341 AF XY: 0.559 AC XY: 2358AN XY: 4216
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GnomAD4 exome AF: 0.537 AC: 132457AN: 246792Hom.: 37016 Cov.: 0 AF XY: 0.541 AC XY: 67622AN XY: 125090
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GnomAD4 genome ? AF: 0.544 AC: 82721AN: 152006Hom.: 22985 Cov.: 32 AF XY: 0.534 AC XY: 39639AN XY: 74288
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at