rs17286683
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 5-140401510-A-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 158,782 control chromosomes in the GnomAD database, including 3,408 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 0.18 ( 3236 hom., cov: 32)
Exomes 𝑓: 0.21 ( 172 hom. )
Consequence
ANKHD1-DT
ENST00000666403.1 upstream_gene
ENST00000666403.1 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0480
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=-0.61).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 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 |
---|---|---|---|---|---|---|---|---|---|
ANKHD1-DT | ENST00000666403.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.181 AC: 27549AN: 152140Hom.: 3227 Cov.: 32
GnomAD3 genomes
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152140
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32
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GnomAD4 exome AF: 0.215 AC: 1401AN: 6524Hom.: 172 AF XY: 0.223 AC XY: 794AN XY: 3568
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GnomAD4 genome ? AF: 0.181 AC: 27565AN: 152258Hom.: 3236 Cov.: 32 AF XY: 0.184 AC XY: 13674AN XY: 74446
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27565
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989
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3478
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