13-95722132-C-T

Position:

• chr13-95722132-C-T

Variant summary

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

The NM_006260.5(DNAJC3):​c.194-1110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,048 control chromosomes in the GnomAD database, including 28,618 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 0.60 (28618 hom., cov: 32)
• Consequence: DNAJC3 NM_006260.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477

Genes affected

DNAJC3 (HGNC:9439): (DnaJ heat shock protein family (Hsp40) member C3) This gene encodes a protein with multiple tetratricopeptide repeat (TPR) motifs as well as the highly conserved J domain found in DNAJ chaperone family members. It is a member of the tetratricopeptide repeat family of proteins and acts as an inhibitor of the interferon-induced, dsRNA-activated protein kinase (PKR). [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC3	NM_006260.5	c.194-1110C>T		intron_variant		ENST00000602402.6	NP_006251.1
DNAJC3	XM_011521104.3	c.194-1110C>T		intron_variant			XP_011519406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC3	ENST00000602402.6	c.194-1110C>T		intron_variant		1	NM_006260.5	ENSP00000473631.1
DNAJC3	ENST00000376795.6	c.194-1110C>T		intron_variant		5		ENSP00000365991.6

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91308 AN: 151930 Hom.: 28575 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.601 AC: 91409 AN: 152048 Hom.: 28618 Cov.: 32 AF XY: 0.603 AC XY: 44817 AN XY: 74312

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.584

Alfa AF: 0.519 Hom.: 40574

Bravo AF: 0.608

Asia WGS AF: 0.656 AC: 2282 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.80

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: rs9302083; hg19: chr13-96374386;