rs931794
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001013619.4(HYKK):c.*168G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 590,018 control chromosomes in the GnomAD database, including 134,807 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 0.69 ( 36603 hom., cov: 32)
Exomes 𝑓: 0.67 ( 98204 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: 0.112
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYKK | NM_001013619.4 | c.*168G>A | 3_prime_UTR_variant | 5/5 | ENST00000388988.9 | ||
HYKK | NM_001083612.2 | c.662-3462G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYKK | ENST00000388988.9 | c.*168G>A | 3_prime_UTR_variant | 5/5 | 5 | NM_001013619.4 | P1 | ||
HYKK | ENST00000569878.5 | c.*168G>A | 3_prime_UTR_variant | 4/4 | 5 | P1 | |||
HYKK | ENST00000408962.6 | c.662-3462G>A | intron_variant | 5 | |||||
HYKK | ENST00000563233.2 | c.662-3462G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.691 AC: 105018AN: 151954Hom.: 36564 Cov.: 32
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GnomAD4 exome AF: 0.668 AC: 292427AN: 437946Hom.: 98204 Cov.: 4 AF XY: 0.672 AC XY: 154495AN XY: 229922
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GnomAD4 genome ? AF: 0.691 AC: 105111AN: 152072Hom.: 36603 Cov.: 32 AF XY: 0.696 AC XY: 51707AN XY: 74336
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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