15-40783204-C-T

Variant names:

• chr15-40783204-C-T
• rs3092985
• NM_018163.3:c.79-3207G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018163.3(DNAJC17):​c.79-3207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,040 control chromosomes in the GnomAD database, including 24,455 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 0.56 (24455 hom., cov: 32)
• Consequence: DNAJC17 NM_018163.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018163.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC17	NM_018163.3	MANE Select	c.79-3207G>A		intron	N/A	NP_060633.1	Q9NVM6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC17	ENST00000220496.9	TSL:1 MANE Select	c.79-3207G>A		intron	N/A	ENSP00000220496.4	Q9NVM6
	DNAJC17	ENST00000559310.3	TSL:1	n.79-3207G>A		intron	N/A	ENSP00000454082.1	H0YLQ7
	DNAJC17	ENST00000560301.5	TSL:1	n.110-3207G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84338 AN: 151922 Hom.: 24399 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.555 AC: 84455 AN: 152040 Hom.: 24455 Cov.: 32 AF XY: 0.557 AC XY: 41371 AN XY: 74312

African (AFR) AF: 0.717 AC: 29746 AN: 41486

American (AMR) AF: 0.456 AC: 6966 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2127 AN: 5178

South Asian (SAS) AF: 0.651 AC: 3135 AN: 4812

European-Finnish (FIN) AF: 0.546 AC: 5767 AN: 10564

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33249 AN: 67954

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.574 Hom.: 3768

Bravo AF: 0.546

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.21
PhyloP100		-0.073
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: rs3092985; hg19: chr15-41075402;