15-43801560-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_016400.4(HYPK):c.261G>A(p.Leu87=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,613,908 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 33 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 53 hom. )
Consequence
HYPK
NM_016400.4 synonymous
NM_016400.4 synonymous
Scores
1
2
12
Clinical Significance
Conservation
PhyloP100: 0.605
Genes affected
HYPK (HGNC:18418): (huntingtin interacting protein K) Enables protein N-terminus binding activity. Involved in negative regulation of apoptotic process and protein stabilization. Located in cytoplasm; microtubule cytoskeleton; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017516911).
BP6
?
Variant 15-43801560-G-A is Benign according to our data. Variant chr15-43801560-G-A is described in ClinVar as [Benign]. Clinvar id is 714534.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.605 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0126 (1915/152294) while in subpopulation AFR AF= 0.0437 (1818/41564). AF 95% confidence interval is 0.0421. There are 33 homozygotes in gnomad4. There are 912 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 33 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYPK | NM_016400.4 | c.261G>A | p.Leu87= | synonymous_variant | 3/4 | ENST00000442995.4 | |
SERF2-C15ORF63 | NR_037673.1 | n.906G>A | non_coding_transcript_exon_variant | 5/6 | |||
HYPK | NM_001199885.1 | c.229G>A | p.Gly77Arg | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYPK | ENST00000442995.4 | c.261G>A | p.Leu87= | synonymous_variant | 3/4 | 1 | NM_016400.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0125 AC: 1898AN: 152176Hom.: 32 Cov.: 32
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GnomAD3 exomes AF: 0.00327 AC: 821AN: 251370Hom.: 18 AF XY: 0.00238 AC XY: 324AN XY: 135898
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GnomAD4 exome AF: 0.00123 AC: 1803AN: 1461614Hom.: 53 Cov.: 31 AF XY: 0.00107 AC XY: 775AN XY: 727132
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GnomAD4 genome ? AF: 0.0126 AC: 1915AN: 152294Hom.: 33 Cov.: 32 AF XY: 0.0122 AC XY: 912AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Benign
T
Vest4
MutPred
Gain of MoRF binding (P = 0.0284);
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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