15-78533322-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001013619.4(HYKK):c.774C>G(p.Ser258Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013619.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYKK | ENST00000388988.9 | c.774C>G | p.Ser258Arg | missense_variant | Exon 5 of 5 | 5 | NM_001013619.4 | ENSP00000373640.4 | ||
HYKK | ENST00000569878.5 | c.774C>G | p.Ser258Arg | missense_variant | Exon 4 of 4 | 5 | ENSP00000455459.1 | |||
HYKK | ENST00000408962.6 | c.662-3978C>G | intron_variant | Intron 4 of 4 | 5 | ENSP00000386197.2 | ||||
HYKK | ENST00000563233.2 | c.662-3978C>G | intron_variant | Intron 3 of 3 | 2 | ENSP00000454850.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000641 AC: 16AN: 249540Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135386
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461690Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.774C>G (p.S258R) alteration is located in exon 5 (coding exon 4) of the HYKK gene. This alteration results from a C to G substitution at nucleotide position 774, causing the serine (S) at amino acid position 258 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at