rs4935825
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006597.6(HSPA8):c.-5-328T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 384,710 control chromosomes in the GnomAD database, including 21,784 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 0.28 ( 7387 hom., cov: 32)
Exomes 𝑓: 0.33 ( 14397 hom. )
Consequence
HSPA8
NM_006597.6 intron
NM_006597.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.29
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA8 | NM_006597.6 | c.-5-328T>G | intron_variant | ENST00000534624.6 | |||
HSPA8 | NM_153201.4 | c.-5-328T>G | intron_variant | ||||
HSPA8 | XM_011542798.2 | c.-5-328T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA8 | ENST00000534624.6 | c.-5-328T>G | intron_variant | 1 | NM_006597.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.279 AC: 42350AN: 151906Hom.: 7386 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
42350
AN:
151906
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.332 AC: 77298AN: 232686Hom.: 14397 Cov.: 0 AF XY: 0.329 AC XY: 41246AN XY: 125398
GnomAD4 exome
AF:
AC:
77298
AN:
232686
Hom.:
Cov.:
0
AF XY:
AC XY:
41246
AN XY:
125398
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.279 AC: 42352AN: 152024Hom.: 7387 Cov.: 32 AF XY: 0.271 AC XY: 20140AN XY: 74302
GnomAD4 genome
?
AF:
AC:
42352
AN:
152024
Hom.:
Cov.:
32
AF XY:
AC XY:
20140
AN XY:
74302
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
493
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at