rs2289218

Variant names:

• chr15-40773528-T-A
• rs2289218
• NM_018163.3:c.792+199A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-40773528-T-A
• chr15-40773528-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DNAJC17	NM_018163.3	c.792+199A>T		intron_variant	Intron 10 of 10	ENST00000220496.9	NP_060633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC17	ENST00000220496.9	c.792+199A>T		intron_variant	Intron 10 of 10	1	NM_018163.3	ENSP00000220496.4
DNAJC17	ENST00000559238.5	n.*820+199A>T		intron_variant	Intron 11 of 11	5		ENSP00000453354.1
DNAJC17	ENST00000561110.5	n.339+199A>T		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.306 AC: 12675 AN: 41410

American (AMR) AF: 0.394 AC: 6019 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1616 AN: 3464

East Asian (EAS) AF: 0.363 AC: 1867 AN: 5140

South Asian (SAS) AF: 0.564 AC: 2714 AN: 4814

European-Finnish (FIN) AF: 0.546 AC: 5769 AN: 10570

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32329 AN: 67866

Other (OTH) AF: 0.418 AC: 882 AN: 2108

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
PhyloP100		-3.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2289218; hg19: chr15-41065726;