rs16836477
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001321623.1(HYCC2):c.832-313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,142 control chromosomes in the GnomAD database, including 4,439 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 0.22 ( 4439 hom., cov: 32)
Consequence
HYCC2
NM_001321623.1 intron
NM_001321623.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.713
Genes affected
HYCC2 (HGNC:28593): (hyccin PI4KA lipid kinase complex subunit 2) Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Predicted to be located in cytosol. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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 (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYCC2 | NM_001321623.1 | c.832-313T>C | intron_variant | ENST00000681958.1 | |||
LOC105373835 | XR_007088050.1 | n.200-20252A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYCC2 | ENST00000681958.1 | c.832-313T>C | intron_variant | NM_001321623.1 | P3 | ||||
HYCC2 | ENST00000418596.7 | c.832-313T>C | intron_variant | 1 | A1 | ||||
HYCC2 | ENST00000286181.7 | c.*585-313T>C | intron_variant, NMD_transcript_variant | 1 | |||||
ENST00000413848.1 | n.369-20252A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.217 AC: 32957AN: 152022Hom.: 4431 Cov.: 32
GnomAD3 genomes
?
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152022
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.217 AC: 33001AN: 152142Hom.: 4439 Cov.: 32 AF XY: 0.212 AC XY: 15805AN XY: 74410
GnomAD4 genome
?
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33001
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152142
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32
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15805
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74410
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233
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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
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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