19-14515385-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The NM_006145.3(DNAJB1):​c.*555C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 153,254 control chromosomes in the GnomAD database, including 333 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 0.061 ( 331 hom., cov: 32)
Exomes 𝑓: 0.053 ( 2 hom. )

Consequence

DNAJB1
NM_006145.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.64
Variant links:
Genes affected
DNAJB1 (HGNC:5270): (DnaJ heat shock protein family (Hsp40) member B1) This gene encodes a member of the DnaJ or Hsp40 (heat shock protein 40 kD) family of proteins. DNAJ family members are characterized by a highly conserved amino acid stretch called the 'J-domain' and function as one of the two major classes of molecular chaperones involved in a wide range of cellular events, such as protein folding and oligomeric protein complex assembly. The encoded protein is a molecular chaperone that stimulates the ATPase activity of Hsp70 heat-shock proteins in order to promote protein folding and prevent misfolded protein aggregation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.17).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0771 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DNAJB1NM_006145.3 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 3/3 ENST00000254322.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DNAJB1ENST00000254322.3 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 3/31 NM_006145.3 P1P25685-1

Frequencies

GnomAD3 genomes
AF:
0.0610
AC:
9284
AN:
152146
Hom.:
331
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0796
Gnomad AMI
AF:
0.158
Gnomad AMR
AF:
0.0497
Gnomad ASJ
AF:
0.0469
Gnomad EAS
AF:
0.00231
Gnomad SAS
AF:
0.0211
Gnomad FIN
AF:
0.0632
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0583
Gnomad OTH
AF:
0.0752
GnomAD4 exome
AF:
0.0525
AC:
52
AN:
990
Hom.:
2
Cov.:
0
AF XY:
0.0592
AC XY:
36
AN XY:
608
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0352
Gnomad4 FIN exome
AF:
0.0498
Gnomad4 NFE exome
AF:
0.0640
Gnomad4 OTH exome
AF:
0.0714
GnomAD4 genome
AF:
0.0610
AC:
9286
AN:
152264
Hom.:
331
Cov.:
32
AF XY:
0.0596
AC XY:
4439
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0794
Gnomad4 AMR
AF:
0.0496
Gnomad4 ASJ
AF:
0.0469
Gnomad4 EAS
AF:
0.00231
Gnomad4 SAS
AF:
0.0211
Gnomad4 FIN
AF:
0.0632
Gnomad4 NFE
AF:
0.0583
Gnomad4 OTH
AF:
0.0744
Alfa
AF:
0.0557
Hom.:
93
Bravo
AF:
0.0623
Asia WGS
AF:
0.0200
AC:
71
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.17
CADD
Benign
16
DANN
Benign
0.93
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1803768; hg19: chr19-14626197; API