rs12916999
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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.*900C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,084 control chromosomes in the GnomAD database, including 8,579 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 0.32 ( 8577 hom., cov: 31)
Exomes 𝑓: 0.29 ( 2 hom. )
Consequence
HYKK
NM_001013619.4 3_prime_UTR
NM_001013619.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.273
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 (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYKK | NM_001013619.4 | c.*900C>T | 3_prime_UTR_variant | 5/5 | ENST00000388988.9 | ||
HYKK | NM_001083612.2 | c.662-2730C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYKK | ENST00000388988.9 | c.*900C>T | 3_prime_UTR_variant | 5/5 | 5 | NM_001013619.4 | P1 | ||
HYKK | ENST00000569878.5 | c.*900C>T | 3_prime_UTR_variant | 4/4 | 5 | P1 | |||
HYKK | ENST00000408962.6 | c.662-2730C>T | intron_variant | 5 | |||||
HYKK | ENST00000563233.2 | c.662-2730C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.315 AC: 47933AN: 151940Hom.: 8579 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.292 AC: 7AN: 24Hom.: 2 Cov.: 0 AF XY: 0.375 AC XY: 6AN XY: 16
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GnomAD4 genome ? AF: 0.315 AC: 47944AN: 152060Hom.: 8577 Cov.: 31 AF XY: 0.313 AC XY: 23227AN XY: 74320
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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