chr17-30247831-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000577420.1(ENSG00000266120):n.61-4243T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,046 control chromosomes in the GnomAD database, including 23,604 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 0.53 ( 23604 hom., cov: 31)
Consequence
ENSG00000266120
ENST00000577420.1 intron
ENST00000577420.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.18
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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105371720 | XR_001752824.2 | n.892-1956T>C | intron_variant | |||||
LOC105371720 | XR_007065695.1 | n.756-1956T>C | intron_variant | |||||
LOC105371720 | XR_007065698.1 | n.756-4243T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000266120 | ENST00000577420.1 | n.61-4243T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.533 AC: 81006AN: 151928Hom.: 23544 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.534 AC: 81131AN: 152046Hom.: 23604 Cov.: 31 AF XY: 0.530 AC XY: 39389AN XY: 74318
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at