chr5-138556533-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_004134.7(HSPA9):c.1881C>T(p.Ser627=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000907 in 1,613,842 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00086 ( 6 hom. )
Consequence
HSPA9
NM_004134.7 synonymous
NM_004134.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0930
Genes affected
HSPA9 (HGNC:5244): (heat shock protein family A (Hsp70) member 9) This gene encodes a member of the heat shock protein 70 gene family. The encoded protein is primarily localized to the mitochondria but is also found in the endoplasmic reticulum, plasma membrane and cytoplasmic vesicles. This protein is a heat-shock cognate protein. This protein plays a role in cell proliferation, stress response and maintenance of the mitochondria. A pseudogene of this gene is found on chromosome 2.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 5-138556533-G-A is Benign according to our data. Variant chr5-138556533-G-A is described in ClinVar as [Benign]. Clinvar id is 788988.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.093 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00135 (205/152156) while in subpopulation EAS AF= 0.00405 (21/5180). AF 95% confidence interval is 0.00272. There are 0 homozygotes in gnomad4. There are 107 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 205 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA9 | NM_004134.7 | c.1881C>T | p.Ser627= | synonymous_variant | 16/17 | ENST00000297185.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA9 | ENST00000297185.9 | c.1881C>T | p.Ser627= | synonymous_variant | 16/17 | 1 | NM_004134.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00135 AC: 205AN: 152040Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00137 AC: 344AN: 250960Hom.: 1 AF XY: 0.00124 AC XY: 168AN XY: 135608
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GnomAD4 exome AF: 0.000861 AC: 1259AN: 1461686Hom.: 6 Cov.: 33 AF XY: 0.000849 AC XY: 617AN XY: 727140
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GnomAD4 genome AF: 0.00135 AC: 205AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74376
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at