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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015291.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DNAJC16	NM_015291.4	MANE Select	c.575-2202A>G	intron	N/A	NP_056106.1	Q9Y2G8-1
DNAJC16	NM_001287811.2		c.-362-2202A>G	intron	N/A	NP_001274740.1	Q9Y2G8-2
SCARNA21B	NR_135613.1		n.32A>G	non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DNAJC16	ENST00000375847.8	TSL:1 MANE Select	c.575-2202A>G	intron	N/A	ENSP00000365007.3	Q9Y2G8-1
DNAJC16	ENST00000375849.5	TSL:1	c.575-2202A>G	intron	N/A	ENSP00000365009.1	Q5TDH4
DNAJC16	ENST00000616884.4	TSL:1	c.-362-2202A>G	intron	N/A	ENSP00000480224.1	Q9Y2G8-2

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over