1-15542197-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

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]

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

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC16	NM_015291.4	c.575-2202A>G		intron_variant		ENST00000375847.8
SCARNA21B	NR_135613.1	n.32A>G		non_coding_transcript_exon_variant	1/1
DNAJC16	NM_001287811.2	c.-362-2202A>G		intron_variant
DNAJC16	NR_109898.2	n.704-2202A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC16	ENST00000375847.8	c.575-2202A>G		intron_variant		1	NM_015291.4	P1
SCARNA21B	ENST00000516057.1	n.33A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40268 AN: 151190 Hom.: 6249 Cov.: 32

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: 40 AN: 174 Hom.: 6 Cov.: 0 AF XY: 0.246 AC XY: 28 AN XY: 114

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.266 AC: 40267 AN: 151310 Hom.: 6253 Cov.: 32 AF XY: 0.271 AC XY: 20035 AN XY: 73984

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.249

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
Dann	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs7516435; hg19: chr1-15868692;