rs1325607

chr1-65285377-C-Achr1-65285377-C-Gchr1-65285377-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000395325.7(DNAJC6):c.22+20445C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,058 control chromosomes in the GnomAD database, including 44,517 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 0.76 (44517 hom., cov: 32)
• Consequence: DNAJC6 ENST00000395325.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724416	XR_007066155.1	n.894-7078G>T		intron_variant, non_coding_transcript_variant
DNAJC6	NM_001256865.2	c.-131+20445C>A		intron_variant
DNAJC6	NM_014787.4	c.22+20445C>A		intron_variant
LOC102724416	XR_007066154.1	n.894-5499G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435739.1	n.90-5499G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115479 AN: 151938 Hom.: 44489 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.760 AC: 115562 AN: 152058 Hom.: 44517 Cov.: 32 AF XY: 0.763 AC XY: 56686 AN XY: 74340

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.783

Alfa AF: 0.784 Hom.: 21361

Bravo AF: 0.761

Asia WGS AF: 0.932 AC: 3240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.61
Dann	Benign	0.62

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: rs1325607; hg19: chr1-65751060;