1-65309229-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000395325.7(DNAJC6):c.22+44297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 151,688 control chromosomes in the GnomAD database, including 320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.059 (320 hom., cov: 30)
• Consequence: DNAJC6 ENST00000395325.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0260

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]

LOC102724416 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 1-65309229-C-T is Benign according to our data. Variant chr1-65309229-C-T is described in ClinVar as [Benign]. Clinvar id is 1290812.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724416	XR_007066155.1	n.6G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC6	ENST00000395325.7	c.22+44297C>T		intron_variant		1		A1
DNAJC6	ENST00000263441.11	c.-130-36382C>T		intron_variant		2		A1
DNAJC6	ENST00000494710.6	c.115+54580C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0587 AC: 8904 AN: 151568 Hom.: 323 Cov.: 30

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.0826

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.0710

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0577

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0587 AC: 8898 AN: 151688 Hom.: 320 Cov.: 30 AF XY: 0.0571 AC XY: 4234 AN XY: 74138

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.000391

Gnomad4 SAS AF: 0.0281

Gnomad4 FIN AF: 0.0710

Gnomad4 NFE AF: 0.0788

Gnomad4 OTH AF: 0.0566

Alfa AF: 0.0687 Hom.: 43

Bravo AF: 0.0552

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	12
Dann	Benign	0.74

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

Other links and lift over

dbSNP: rs75992237; hg19: chr1-65774912;