Variant rs2301176 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018163.3(DNAJC17):c.*751A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 1,457,468 control chromosomes in the GnomAD database, including 1,869 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 0.069 ( 526 hom., cov: 33)

Exomes 𝑓: 0.040 ( 1343 hom. )

Consequence

DNAJC17
NM_018163.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.208

Variant links:

Genes affected

DNAJC17 (HGNC:25556): (DnaJ heat shock protein family (Hsp40) member C17) Predicted to enable RNA binding activity. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and toxin transport. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC17 links:

GCHFR (HGNC:4194): (GTP cyclohydrolase I feedback regulator) GTP cyclohydrolase I feedback regulatory protein binds to and mediates tetrahydrobiopterin inhibition of GTP cyclohydrolase I. The regulatory protein, GCHFR, consists of a homodimer. It is postulated that GCHFR may play a role in regulating phenylalanine metabolism in the liver and in the production of biogenic amine neurotransmitters and nitric oxide. [provided by RefSeq, Jul 2008]

GCHFR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC17	NM_018163.3 link	c.*751A>G		3_prime_UTR_variant	11/11	ENST00000220496.9	NP_060633.1	Q9NVM6
GCHFR	NM_005258.3 link	c.132-37T>C		intron_variant		ENST00000260447.6	NP_005249.1	P30047-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC17	ENST00000220496 link	c.*751A>G		3_prime_UTR_variant	11/11	1	NM_018163.3	ENSP00000220496.4		Q9NVM6
GCHFR	ENST00000260447.6 link	c.132-37T>C		intron_variant		1	NM_005258.3	ENSP00000260447.4		P30047-1

Frequencies

GnomAD3 genomes

AF:

0.0686

AC:

10388

AN:

151534

Hom.:

524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0566

Gnomad ASJ

AF:

0.0669

Gnomad EAS

AF:

0.0260

Gnomad SAS

AF:

0.0739

Gnomad FIN

AF:

0.0220

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0376

Gnomad OTH

AF:

0.0737

GnomAD3 exomes

AF:

0.0456

AC:

6562

AN:

143918

Hom.:

235

AF XY:

0.0443

AC XY:

3433

AN XY:

77488

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.0298

Gnomad ASJ exome

AF:

0.0563

Gnomad EAS exome

AF:

0.0215

Gnomad SAS exome

AF:

0.0685

Gnomad FIN exome

AF:

0.0235

Gnomad NFE exome

AF:

0.0396

Gnomad OTH exome

AF:

0.0473

GnomAD4 exome

AF:

0.0405

AC:

52863

AN:

1305818

Hom.:

1343

Cov.:

AF XY:

0.0408

AC XY:

25964

AN XY:

637010

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.0369

Gnomad4 ASJ exome

AF:

0.0628

Gnomad4 EAS exome

AF:

0.0286

Gnomad4 SAS exome

AF:

0.0611

Gnomad4 FIN exome

AF:

0.0247

Gnomad4 NFE exome

AF:

0.0369

Gnomad4 OTH exome

AF:

0.0482

GnomAD4 genome

AF:

0.0686

AC:

10406

AN:

151650

Hom.:

526

Cov.:

AF XY:

0.0668

AC XY:

4954

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0564

Gnomad4 ASJ

AF:

0.0669

Gnomad4 EAS

AF:

0.0261

Gnomad4 SAS

AF:

0.0731

Gnomad4 FIN

AF:

0.0220

Gnomad4 NFE

AF:

0.0376

Gnomad4 OTH

AF:

0.0729

Alfa

AF:

0.0549

Hom.:

104

Bravo

AF:

0.0731

Asia WGS

AF:

0.0580

AC:

203

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.2

DANN

Benign

0.70

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over