rs34397183
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005345.6(HSPA1A):c.-191G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,378,072 control chromosomes in the GnomAD database, including 31 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 0.0077 ( 20 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 11 hom. )
Consequence
HSPA1A
NM_005345.6 5_prime_UTR
NM_005345.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.29
Genes affected
HSPA1A (HGNC:5232): (heat shock protein family A (Hsp70) member 1A) This intronless gene encodes a 70kDa heat shock protein which is a member of the heat shock protein 70 family. In conjuction with other heat shock proteins, this protein stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. It is also involved in the ubiquitin-proteasome pathway through interaction with the AU-rich element RNA-binding protein 1. The gene is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which encode similar proteins. [provided by RefSeq, Jul 2008]
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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=-0.48).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0077 (1173/152352) while in subpopulation AFR AF= 0.0267 (1108/41572). AF 95% confidence interval is 0.0253. There are 20 homozygotes in gnomad4. There are 527 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1173 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA1A | NM_005345.6 | c.-191G>A | 5_prime_UTR_variant | 1/1 | ENST00000375651.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA1A | ENST00000375651.7 | c.-191G>A | 5_prime_UTR_variant | 1/1 | NM_005345.6 | P1 | |||
HSPA1A | ENST00000608703.1 | c.-191G>A | 5_prime_UTR_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00768 AC: 1169AN: 152234Hom.: 20 Cov.: 32
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GnomAD4 exome AF: 0.000953 AC: 1168AN: 1225720Hom.: 11 Cov.: 19 AF XY: 0.000848 AC XY: 520AN XY: 613398
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GnomAD4 genome ? AF: 0.00770 AC: 1173AN: 152352Hom.: 20 Cov.: 32 AF XY: 0.00707 AC XY: 527AN XY: 74502
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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