rs2276075
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006597.6(HSPA8):c.-36C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0642 in 152,844 control chromosomes in the GnomAD database, including 379 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 0.064 ( 376 hom., cov: 33)
Exomes 𝑓: 0.055 ( 3 hom. )
Consequence
HSPA8
NM_006597.6 5_prime_UTR
NM_006597.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.62
Genes affected
HSPA8 (HGNC:5241): (heat shock protein family A (Hsp70) member 8) This gene encodes a member of the heat shock protein 70 family, which contains both heat-inducible and constitutively expressed members. This protein belongs to the latter group, which are also referred to as heat-shock cognate proteins. It functions as a chaperone, and binds to nascent polypeptides to facilitate correct folding. It also functions as an ATPase in the disassembly of clathrin-coated vesicles during transport of membrane components through the cell. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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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 (AMR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA8 | NM_006597.6 | c.-36C>T | 5_prime_UTR_variant | 1/9 | ENST00000534624.6 | ||
HSPA8 | NM_153201.4 | c.-36C>T | 5_prime_UTR_variant | 1/8 | |||
HSPA8 | XM_011542798.2 | c.-6+253C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA8 | ENST00000534624.6 | c.-36C>T | 5_prime_UTR_variant | 1/9 | 1 | NM_006597.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0642 AC: 9763AN: 152004Hom.: 376 Cov.: 33
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GnomAD4 exome AF: 0.0554 AC: 40AN: 722Hom.: 3 Cov.: 0 AF XY: 0.0566 AC XY: 31AN XY: 548
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GnomAD4 genome ? AF: 0.0643 AC: 9775AN: 152122Hom.: 376 Cov.: 33 AF XY: 0.0685 AC XY: 5094AN XY: 74344
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at