rs1345043761

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_025219.3(DNAJC5):​c.-51_-44delCGGAGCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 146,304 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 32)

Consequence

DNAJC5
NM_025219.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.91
Variant links:
Genes affected
DNAJC5 (HGNC:16235): (DnaJ heat shock protein family (Hsp40) member C5) This gene is a member of the J protein family. J proteins function in many cellular processes by regulating the ATPase activity of 70 kDa heat shock proteins. The encoded protein plays a role in membrane trafficking and protein folding, and has been shown to have anti-neurodegenerative properties. The encoded protein is known to play a role in cystic fibrosis and Huntington's disease. A pseudogene of this gene is located on the short arm of chromosome 8. [provided by RefSeq, Nov 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAJC5NM_025219.3 linkc.-51_-44delCGGAGCCG 5_prime_UTR_variant Exon 1 of 5 ENST00000360864.9 NP_079495.1 Q9H3Z4-1Q6AHX3
DNAJC5XM_047440509.1 linkc.-1736_-1729delCGGAGCCG 5_prime_UTR_variant Exon 1 of 5 XP_047296465.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAJC5ENST00000360864 linkc.-51_-44delCGGAGCCG 5_prime_UTR_variant Exon 1 of 5 1 NM_025219.3 ENSP00000354111.4 Q9H3Z4-1
DNAJC5ENST00000470551.1 linkn.-51_-44delCGGAGCCG non_coding_transcript_exon_variant Exon 1 of 6 2 ENSP00000434744.1 Q9H3Z4-2
DNAJC5ENST00000470551.1 linkn.-51_-44delCGGAGCCG 5_prime_UTR_variant Exon 1 of 6 2 ENSP00000434744.1 Q9H3Z4-2
ENSG00000290226ENST00000703636.1 linkn.453+12464_453+12471delCGGAGCCG intron_variant Intron 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.0000137
AC:
2
AN:
146304
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000197
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000152
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000137
AC:
2
AN:
146304
Hom.:
0
Cov.:
32
AF XY:
0.0000140
AC XY:
1
AN XY:
71206
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000197
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000152
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs1345043761; hg19: chr20-62526627; API