Variant rs2236215 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015291.4(DNAJC16):c.1600A>C(p.Arg534Arg) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,612,318 control chromosomes in the GnomAD database, including 58,765 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 10668 hom., cov: 30)

Exomes 𝑓: 0.25 ( 48097 hom. )

Consequence

DNAJC16
NM_015291.4 splice_region, synonymous

Scores

Splicing: ADA: 0.0007144

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48

Variant links:

Genes affected

DNAJC16 (HGNC:29157): (DnaJ heat shock protein family (Hsp40) member C16) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC16 links:

DNAJC16 (HGNC:):

DNAJC16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP7

Synonymous conserved (PhyloP=1.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC16	NM_015291.4 linkuse as main transcript	c.1600A>C	p.Arg534Arg	splice_region_variant, synonymous_variant	12/15	ENST00000375847.8	NP_056106.1	Q9Y2G8-1
DNAJC16	NM_001287811.2 linkuse as main transcript	c.664A>C	p.Arg222Arg	splice_region_variant, synonymous_variant	11/14		NP_001274740.1	Q9Y2G8-2
DNAJC16	NR_109898.2 linkuse as main transcript	n.1729A>C		splice_region_variant, non_coding_transcript_exon_variant	12/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC16	ENST00000375847.8 linkuse as main transcript	c.1600A>C	p.Arg534Arg	splice_region_variant, synonymous_variant	12/15	1	NM_015291.4	ENSP00000365007.3		Q9Y2G8-1

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51199

AN:

151548

Hom.:

10632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.584

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.0648

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.312

GnomAD3 exomes

AF:

0.246

AC:

61871

AN:

251038

Hom.:

9140

AF XY:

0.244

AC XY:

33055

AN XY:

135714

show subpopulations

Gnomad AFR exome

AF:

0.576

Gnomad AMR exome

AF:

0.144

Gnomad ASJ exome

AF:

0.276

Gnomad EAS exome

AF:

0.0655

Gnomad SAS exome

AF:

0.221

Gnomad FIN exome

AF:

0.299

Gnomad NFE exome

AF:

0.253

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.248

AC:

361884

AN:

1460652

Hom.:

48097

Cov.:

AF XY:

0.247

AC XY:

179223

AN XY:

726752

show subpopulations

Gnomad4 AFR exome

AF:

0.589

Gnomad4 AMR exome

AF:

0.152

Gnomad4 ASJ exome

AF:

0.280

Gnomad4 EAS exome

AF:

0.0773

Gnomad4 SAS exome

AF:

0.215

Gnomad4 FIN exome

AF:

0.299

Gnomad4 NFE exome

AF:

0.246

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.338

AC:

51280

AN:

151666

Hom.:

10668

Cov.:

AF XY:

0.334

AC XY:

24777

AN XY:

74100

show subpopulations

Gnomad4 AFR

AF:

0.585

Gnomad4 AMR

AF:

0.223

Gnomad4 ASJ

AF:

0.272

Gnomad4 EAS

AF:

0.0650

Gnomad4 SAS

AF:

0.187

Gnomad4 FIN

AF:

0.304

Gnomad4 NFE

AF:

0.256

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.266

Hom.:

5560

Bravo

AF:

0.343

Asia WGS

AF:

0.175

AC:

606

AN:

3478

EpiCase

AF:

0.253

EpiControl

AF:

0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00071

dbscSNV1_RF

Benign

0.0040

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