Genetic Variant DNAJC16:c.575-2202A>G (chr1-15542197-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015291.4(DNAJC16):c.575-2202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,484 control chromosomes in the GnomAD database, including 6,259 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 0.27 ( 6253 hom., cov: 32)

Exomes 𝑓: 0.23 ( 6 hom. )

Consequence

DNAJC16
NM_015291.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.241

Publications

10 publications found

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:

SCARNA21B (HGNC:52237): (small Cajal body-specific RNA 21B)

SCARNA21B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
DNAJC16	NM_015291.4 link	c.575-2202A>G	intron_variant	Intron 4 of 14	ENST00000375847.8	NP_056106.1	Q9Y2G8-1
SCARNA21B	NR_135613.1 link	n.32A>G	non_coding_transcript_exon_variant	Exon 1 of 1
DNAJC16	NM_001287811.2 link	c.-362-2202A>G	intron_variant	Intron 3 of 13		NP_001274740.1	Q9Y2G8-2
DNAJC16	NR_109898.2 link	n.704-2202A>G	intron_variant	Intron 4 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC16	ENST00000375847.8 link	c.575-2202A>G		intron_variant	Intron 4 of 14	1	NM_015291.4	ENSP00000365007.3		Q9Y2G8-1

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40268

AN:

151190

Hom.:

6249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.583

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.277

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.249

GnomAD4 exome

AF:

0.230

AC:

AN:

174

Hom.:

Cov.:

AF XY:

0.246

AC XY:

AN XY:

114

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.229

AC:

AN:

144

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.266

AC:

40267

AN:

151310

Hom.:

6253

Cov.:

AF XY:

0.271

AC XY:

20035

AN XY:

73984

show subpopulations

African (AFR)

AF:

0.124

AC:

5099

AN:

41140

American (AMR)

AF:

0.294

AC:

4470

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

853

AN:

3454

East Asian (EAS)

AF:

0.582

AC:

3003

AN:

5156

South Asian (SAS)

AF:

0.245

AC:

1176

AN:

4802

European-Finnish (FIN)

AF:

0.370

AC:

3895

AN:

10526

Middle Eastern (MID)

AF:

0.279

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.308

AC:

20868

AN:

67706

Other (OTH)

AF:

0.249

AC:

524

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1456

2912

4369

5825

7281

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.273

Hom.:

742

Bravo

AF:

0.253

Asia WGS

AF:

0.377

AC:

1312

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.7

(source)

DANN

Benign

0.83

PhyloP100

-0.24

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over