chr6-43837625-T-A
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000637813.1(ENSG00000283573):n.366-4886T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,120 control chromosomes in the GnomAD database, including 29,256 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 0.59 ( 29256 hom., cov: 33)
Consequence
ENSG00000283573
ENST00000637813.1 intron
ENST00000637813.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.179
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=-0.71).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105375069 | XR_001744130.1 | n.675+259A>T | intron_variant | |||||
LOC105375070 | XR_007059588.1 | n.193-4886T>A | intron_variant | |||||
LOC105375070 | XR_007059589.1 | n.193-4886T>A | intron_variant | |||||
LOC105375069 | XR_007059590.1 | n.392+259A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000283573 | ENST00000637813.1 | n.366-4886T>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.593 AC: 90074AN: 152002Hom.: 29252 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.592 AC: 90106AN: 152120Hom.: 29256 Cov.: 33 AF XY: 0.597 AC XY: 44400AN XY: 74374
GnomAD4 genome
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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