rs9672189
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001013619.4(HYKK):c.-6+1383A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,054 control chromosomes in the GnomAD database, including 470 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 0.043 ( 470 hom., cov: 32)
Consequence
HYKK
NM_001013619.4 intron
NM_001013619.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.518
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HYKK | NM_001013619.4 | c.-6+1383A>C | intron_variant | ENST00000388988.9 | NP_001013641.2 | |||
HYKK | NM_001083612.2 | c.-6+1383A>C | intron_variant | NP_001077081.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYKK | ENST00000388988.9 | c.-6+1383A>C | intron_variant | 5 | NM_001013619.4 | ENSP00000373640.4 | ||||
HYKK | ENST00000566332.5 | c.-6+1383A>C | intron_variant | 1 | ENSP00000457154.1 | |||||
HYKK | ENST00000408962.6 | c.-6+1383A>C | intron_variant | 5 | ENSP00000386197.2 | |||||
HYKK | ENST00000566289.5 | n.-6+1383A>C | intron_variant | 2 | ENSP00000456614.1 |
Frequencies
GnomAD3 genomes AF: 0.0433 AC: 6583AN: 151940Hom.: 470 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0433 AC: 6590AN: 152054Hom.: 470 Cov.: 32 AF XY: 0.0426 AC XY: 3163AN XY: 74332
GnomAD4 genome
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3163
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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