6-31816809-G-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_005345.6(HSPA1A):c.1053G>A(p.Gln351=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HSPA1A
NM_005345.6 synonymous
NM_005345.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.527
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP7
Synonymous conserved (PhyloP=0.527 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| HSPA1A | NM_005345.6 | c.1053G>A | p.Gln351= | synonymous_variant | 1/1 | ENST00000375651.7 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HSPA1A | ENST00000375651.7 | c.1053G>A | p.Gln351= | synonymous_variant | 1/1 | NM_005345.6 | P1 | ||
| HSPA1A | ENST00000608703.1 | c.558G>A | p.Gln186= | synonymous_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
0
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0150 AC: 1431AN: 95294Hom.: 0 Cov.: 0 AF XY: 0.0151 AC XY: 766AN XY: 50784
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1431
AN:
95294
Hom.:
Cov.:
0
AF XY:
AC XY:
766
AN XY:
50784
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
GnomAD4 genome
Cov.:
0
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Chronic obstructive pulmonary disease Other:1
| association, no assertion criteria provided | case-control | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Aug 04, 2019 | - - |
Computational 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