rs35682610

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_005346.6(HSPA1B):ā€‹c.1710T>Gā€‹(p.Val570=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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: š‘“ 0.016 ( 17 hom., cov: 23)
Exomes š‘“: 0.0030 ( 196 hom. )
Failed GnomAD Quality Control

Consequence

HSPA1B
NM_005346.6 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420
Variant links:
Genes affected
HSPA1B (HGNC:5233): (heat shock protein family A (Hsp70) member 1B) 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=-0.73).
BP7
Synonymous conserved (PhyloP=0.042 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HSPA1BNM_005346.6 linkuse as main transcriptc.1710T>G p.Val570= synonymous_variant 1/1 ENST00000375650.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HSPA1BENST00000375650.5 linkuse as main transcriptc.1710T>G p.Val570= synonymous_variant 1/1 NM_005346.6 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
2434
AN:
151066
Hom.:
17
Cov.:
23
FAILED QC
Gnomad AFR
AF:
0.0263
Gnomad AMI
AF:
0.00439
Gnomad AMR
AF:
0.0138
Gnomad ASJ
AF:
0.0230
Gnomad EAS
AF:
0.0244
Gnomad SAS
AF:
0.0157
Gnomad FIN
AF:
0.00490
Gnomad MID
AF:
0.0192
Gnomad NFE
AF:
0.0114
Gnomad OTH
AF:
0.0168
GnomAD3 exomes
AF:
0.000901
AC:
218
AN:
242016
Hom.:
40
AF XY:
0.000894
AC XY:
118
AN XY:
131960
show subpopulations
Gnomad AFR exome
AF:
0.00220
Gnomad AMR exome
AF:
0.000472
Gnomad ASJ exome
AF:
0.00123
Gnomad EAS exome
AF:
0.00166
Gnomad SAS exome
AF:
0.00151
Gnomad FIN exome
AF:
0.000185
Gnomad NFE exome
AF:
0.000725
Gnomad OTH exome
AF:
0.000167
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00305
AC:
4398
AN:
1444024
Hom.:
196
Cov.:
31
AF XY:
0.00310
AC XY:
2228
AN XY:
718082
show subpopulations
Gnomad4 AFR exome
AF:
0.00748
Gnomad4 AMR exome
AF:
0.00374
Gnomad4 ASJ exome
AF:
0.0112
Gnomad4 EAS exome
AF:
0.0211
Gnomad4 SAS exome
AF:
0.00189
Gnomad4 FIN exome
AF:
0.00253
Gnomad4 NFE exome
AF:
0.00207
Gnomad4 OTH exome
AF:
0.00495
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0161
AC:
2436
AN:
151184
Hom.:
17
Cov.:
23
AF XY:
0.0156
AC XY:
1156
AN XY:
73934
show subpopulations
Gnomad4 AFR
AF:
0.0262
Gnomad4 AMR
AF:
0.0138
Gnomad4 ASJ
AF:
0.0230
Gnomad4 EAS
AF:
0.0244
Gnomad4 SAS
AF:
0.0157
Gnomad4 FIN
AF:
0.00490
Gnomad4 NFE
AF:
0.0114
Gnomad4 OTH
AF:
0.0167
Alfa
AF:
0.0124
Hom.:
7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
9.0
DANN
Benign
0.75
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35682610; hg19: chr6-31797437; COSMIC: COSV65128261; COSMIC: COSV65128261; API