rs2289218

chr15-40773528-T-Achr15-40773528-T-G

Variant summary

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

The NM_018163.3(DNAJC17):c.792+199A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,852 control chromosomes in the GnomAD database, including 14,279 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 0.42 (14279 hom., cov: 31)
• Consequence: DNAJC17 NM_018163.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24

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]

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 (SAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC17	NM_018163.3	c.792+199A>T		intron_variant		ENST00000220496.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC17	ENST00000220496.9	c.792+199A>T		intron_variant		1	NM_018163.3	P1
DNAJC17	ENST00000559238.5	c.*820+199A>T		intron_variant, NMD_transcript_variant		5
DNAJC17	ENST00000561110.5	n.339+199A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64433 AN: 151734 Hom.: 14264 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.412

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.425 AC: 64474 AN: 151852 Hom.: 14279 Cov.: 31 AF XY: 0.430 AC XY: 31920 AN XY: 74222

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.418

Alfa AF: 0.463 Hom.: 2182

Bravo AF: 0.400

Asia WGS AF: 0.507 AC: 1760 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	0.011
Dann	Benign	0.73

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: rs2289218; hg19: chr15-41065726;