Variant 6-31827773-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005346.6(HSPA1B):c.-178C>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 0.0759 in 1,388,778 control chromosomes in the GnomAD database, including 5,920 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.11 ( 1208 hom., cov: 31)

Exomes 𝑓: 0.072 ( 4712 hom. )

Consequence

HSPA1B
NM_005346.6 5_prime_UTR

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -2.05

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]

HSPA1B links:

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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=-0.57).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA1B	NM_005346.6 linkuse as main transcript	c.-178C>T		5_prime_UTR_variant	1/1	ENST00000375650.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA1B	ENST00000375650.5 linkuse as main transcript	c.-178C>T		5_prime_UTR_variant	1/1		NM_005346.6	P1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16169

AN:

152052

Hom.:

1202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0615

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0387

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0675

Gnomad OTH

AF:

0.143

GnomAD3 exomes

AF:

0.0934

AC:

13246

AN:

141746

Hom.:

949

AF XY:

0.0939

AC XY:

7255

AN XY:

77248

show subpopulations

Gnomad AFR exome

AF:

0.194

Gnomad AMR exome

AF:

0.0907

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.0505

Gnomad SAS exome

AF:

0.138

Gnomad FIN exome

AF:

0.0381

Gnomad NFE exome

AF:

0.0688

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.0722

AC:

89239

AN:

1236608

Hom.:

4712

Cov.:

AF XY:

0.0740

AC XY:

45688

AN XY:

617416

show subpopulations

Gnomad4 AFR exome

AF:

0.193

Gnomad4 AMR exome

AF:

0.0953

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.0684

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.0372

Gnomad4 NFE exome

AF:

0.0602

Gnomad4 OTH exome

AF:

0.0946

GnomAD4 genome

AF:

0.106

AC:

16191

AN:

152170

Hom.:

1208

Cov.:

AF XY:

0.105

AC XY:

7840

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.106

Gnomad4 ASJ

AF:

0.166

Gnomad4 EAS

AF:

0.0617

Gnomad4 SAS

AF:

0.126

Gnomad4 FIN

AF:

0.0387

Gnomad4 NFE

AF:

0.0675

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.0759

Hom.:

938

Bravo

AF:

0.117

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

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.25

DANN

Benign

0.83

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over