17-41990222-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003315.4(DNAJC7):​c.599+41delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 1,546,384 control chromosomes in the GnomAD database, including 5,452 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1113 hom., cov: 30)
Exomes 𝑓: 0.072 ( 4339 hom. )

Consequence

DNAJC7
NM_003315.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.17
Variant links:
Genes affected
DNAJC7 (HGNC:12392): (DnaJ heat shock protein family (Hsp40) member C7) This gene encodes a member of the DNAJ heat shock protein 40 family of proteins that is characterized by two N-terminal tetratricopeptide repeat domains and a C-terminal DNAJ domain. This protein binds the chaperone proteins heat shock proteins 70 and 90 in an ATP-dependent manner and may function as a co-chaperone. Pseudogenes of this gene are found on chromosomes 1 and 6. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 17-41990222-TG-T is Benign according to our data. Variant chr17-41990222-TG-T is described in ClinVar as [Benign]. Clinvar id is 1245936.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNAJC7NM_003315.4 linkuse as main transcriptc.599+41delC intron_variant ENST00000457167.9 NP_003306.3 Q99615-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNAJC7ENST00000457167.9 linkuse as main transcriptc.599+41delC intron_variant 1 NM_003315.4 ENSP00000406463.2 Q99615-1

Frequencies

GnomAD3 genomes
AF:
0.107
AC:
16292
AN:
152106
Hom.:
1099
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.199
Gnomad AMI
AF:
0.0548
Gnomad AMR
AF:
0.0586
Gnomad ASJ
AF:
0.0694
Gnomad EAS
AF:
0.136
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.0763
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.0667
Gnomad OTH
AF:
0.100
GnomAD3 exomes
AF:
0.0839
AC:
15313
AN:
182436
Hom.:
804
AF XY:
0.0854
AC XY:
8283
AN XY:
96948
show subpopulations
Gnomad AFR exome
AF:
0.196
Gnomad AMR exome
AF:
0.0429
Gnomad ASJ exome
AF:
0.0749
Gnomad EAS exome
AF:
0.137
Gnomad SAS exome
AF:
0.118
Gnomad FIN exome
AF:
0.0792
Gnomad NFE exome
AF:
0.0663
Gnomad OTH exome
AF:
0.0728
GnomAD4 exome
AF:
0.0721
AC:
100580
AN:
1394160
Hom.:
4339
Cov.:
23
AF XY:
0.0731
AC XY:
50459
AN XY:
690232
show subpopulations
Gnomad4 AFR exome
AF:
0.204
Gnomad4 AMR exome
AF:
0.0448
Gnomad4 ASJ exome
AF:
0.0742
Gnomad4 EAS exome
AF:
0.129
Gnomad4 SAS exome
AF:
0.113
Gnomad4 FIN exome
AF:
0.0756
Gnomad4 NFE exome
AF:
0.0635
Gnomad4 OTH exome
AF:
0.0797
GnomAD4 genome
AF:
0.107
AC:
16353
AN:
152224
Hom.:
1113
Cov.:
30
AF XY:
0.108
AC XY:
8038
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.0583
Gnomad4 ASJ
AF:
0.0694
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.0763
Gnomad4 NFE
AF:
0.0667
Gnomad4 OTH
AF:
0.104
Alfa
AF:
0.0853
Hom.:
99
Bravo
AF:
0.108
Asia WGS
AF:
0.142
AC:
494
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 11, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs145343720; hg19: chr17-40142240; API