1-65405379-G-T

Variant summary

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

The NM_001256864.2(DNAJC6):​c.2228-491G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,138 control chromosomes in the GnomAD database, including 29,177 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 0.59 ( 29177 hom., cov: 33)

Consequence

DNAJC6
NM_001256864.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247
Variant links:
Genes affected
DNAJC6 (HGNC:15469): (DnaJ heat shock protein family (Hsp40) member C6) DNAJC6 belongs to the evolutionarily conserved DNAJ/HSP40 family of proteins, which regulate molecular chaperone activity by stimulating ATPase activity. DNAJ proteins may have up to 3 distinct domains: a conserved 70-amino acid J domain, usually at the N terminus, a glycine/phenylalanine (G/F)-rich region, and a cysteine-rich domain containing 4 motifs resembling a zinc finger domain (Ohtsuka and Hata, 2000 [PubMed 11147971]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAJC6NM_001256864.2 linkc.2228-491G>T intron_variant Intron 15 of 18 ENST00000371069.5 NP_001243793.1 O75061-2
DNAJC6NM_014787.4 linkc.2057-491G>T intron_variant Intron 15 of 18 NP_055602.1 O75061-1
DNAJC6NM_001256865.2 linkc.2018-491G>T intron_variant Intron 16 of 19 NP_001243794.1 O75061-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAJC6ENST00000371069.5 linkc.2228-491G>T intron_variant Intron 15 of 18 1 NM_001256864.2 ENSP00000360108.4 O75061-2
DNAJC6ENST00000395325.7 linkc.2057-491G>T intron_variant Intron 15 of 18 1 ENSP00000378735.3 O75061-1
DNAJC6ENST00000263441.11 linkc.2018-491G>T intron_variant Intron 16 of 19 2 ENSP00000263441.7 O75061-4

Frequencies

GnomAD3 genomes
AF:
0.593
AC:
90073
AN:
152022
Hom.:
29122
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.863
Gnomad AMI
AF:
0.325
Gnomad AMR
AF:
0.563
Gnomad ASJ
AF:
0.499
Gnomad EAS
AF:
0.815
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.457
Gnomad MID
AF:
0.579
Gnomad NFE
AF:
0.449
Gnomad OTH
AF:
0.573
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.593
AC:
90188
AN:
152138
Hom.:
29177
Cov.:
33
AF XY:
0.594
AC XY:
44188
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.863
Gnomad4 AMR
AF:
0.564
Gnomad4 ASJ
AF:
0.499
Gnomad4 EAS
AF:
0.815
Gnomad4 SAS
AF:
0.560
Gnomad4 FIN
AF:
0.457
Gnomad4 NFE
AF:
0.449
Gnomad4 OTH
AF:
0.577
Alfa
AF:
0.488
Hom.:
9666
Bravo
AF:
0.614
Asia WGS
AF:
0.680
AC:
2366
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.8
DANN
Benign
0.17

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: rs913199; hg19: chr1-65871062; API