17-41990103-C-T

Position:

• chr17-41990103-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003315.4(DNAJC7):​c.599+161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,102 control chromosomes in the GnomAD database, including 13,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.41 (13877 hom., cov: 33)
• Consequence: DNAJC7 NM_003315.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.226

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]

DNAJC7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 17-41990103-C-T is Benign according to our data. Variant chr17-41990103-C-T is described in ClinVar as [Benign]. Clinvar id is 1223976.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC7	NM_003315.4	c.599+161G>A		intron_variant		ENST00000457167.9	NP_003306.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC7	ENST00000457167.9	c.599+161G>A		intron_variant		1	NM_003315.4	ENSP00000406463.2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61611 AN: 151984 Hom.: 13877 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.405 AC: 61614 AN: 152102 Hom.: 13877 Cov.: 33 AF XY: 0.405 AC XY: 30098 AN XY: 74338

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.417

Alfa AF: 0.463 Hom.: 3408

Bravo AF: 0.390

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.69

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: rs28618174; hg19: chr17-40142121; COSMIC: COSV57270291; COSMIC: COSV57270291;