chr11-86306418-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_016401.4(HIKESHI):c.204A>G(p.Gln68=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 1,613,872 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
HIKESHI
NM_016401.4 synonymous
NM_016401.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.640
Genes affected
HIKESHI (HGNC:26938): (heat shock protein nuclear import factor hikeshi) This gene encodes an evolutionarily conserved nuclear transport receptor that mediates heat-shock-induced nuclear import of 70 kDa heat-shock proteins (Hsp70s) through interactions with FG-nucleoporins. The protein mediates transport of the ATP form but not the ADP form of Hsp70 proteins under conditions of heat shock stress. Structural analyses demonstrate that the protein forms an asymmetric homodimer and that the N-terminal domain consists of a jelly-roll/beta-sandwich fold structure that contains hydrophobic pockets involved in FG-nucleoporin recognition. Reduction of RNA expression levels in HeLa cells using small interfering RNAs results in inhibition of heat shock-induced nuclear accumulation of Hsp70s, indicating a role for this gene in regulation of Hsp70 nuclear import during heat shock stress. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 11-86306418-A-G is Benign according to our data. Variant chr11-86306418-A-G is described in ClinVar as [Benign]. Clinvar id is 729866.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.64 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIKESHI | NM_016401.4 | c.204A>G | p.Gln68= | synonymous_variant | 2/5 | ENST00000278483.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIKESHI | ENST00000278483.8 | c.204A>G | p.Gln68= | synonymous_variant | 2/5 | 1 | NM_016401.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00189 AC: 287AN: 152116Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000477 AC: 120AN: 251442Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135894
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GnomAD4 exome AF: 0.000165 AC: 241AN: 1461638Hom.: 1 Cov.: 31 AF XY: 0.000154 AC XY: 112AN XY: 727132
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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 | Jan 22, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at